[English] 日本語
Yorodumi
- PDB-7fy8: Crystal Structure of human FABP1 in complex with 2-[[4-cyclopropy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7fy8
TitleCrystal Structure of human FABP1 in complex with 2-[[4-cyclopropyl-5-methyl-3-[3-(trifluoromethyl)-1,2,4-oxadiazol-5-yl]thiophen-2-yl]carbamoyl]cyclopentene-1-carboxylic acid
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN / CYTOPLASM / LIPID-BINDING / TRANSPORT / PROTEIN BINDING
Function / homology
Function and homology information


response to vitamin B3 / oleic acid binding / apical cortex / positive regulation of fatty acid beta-oxidation / bile acid binding / intestinal absorption / Heme degradation / long-chain fatty acid transmembrane transporter activity / heterocyclic compound binding / Triglyceride catabolism ...response to vitamin B3 / oleic acid binding / apical cortex / positive regulation of fatty acid beta-oxidation / bile acid binding / intestinal absorption / Heme degradation / long-chain fatty acid transmembrane transporter activity / heterocyclic compound binding / Triglyceride catabolism / antioxidant activity / peroxisomal matrix / fatty acid transport / Regulation of lipid metabolism by PPARalpha / fatty acid binding / phospholipid binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PPARA activates gene expression / Cytoprotection by HMOX1 / cellular response to hydrogen peroxide / cellular response to hypoxia / chromatin binding / negative regulation of apoptotic process / protein-containing complex / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
Lipocalin / cytosolic fatty-acid binding protein family / Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin
Similarity search - Domain/homology
THIOCYANATE ION / Chem-VI9 / Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsEhler, A. / Benz, J. / Obst, U. / Richter, H. / Rudolph, M.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: To be published
Title: Crystal Structure of a human FABP1 complex
Authors: Obst, U. / Magnone, C. / Kuhn, B. / Rudolph, M.G.
History
DepositionApr 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fatty acid-binding protein, liver
B: Fatty acid-binding protein, liver
C: Fatty acid-binding protein, liver
D: Fatty acid-binding protein, liver
E: Fatty acid-binding protein, liver
F: Fatty acid-binding protein, liver
G: Fatty acid-binding protein, liver
H: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,95324
Polymers116,0698
Non-polymers3,88416
Water7,692427
1
A: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9943
Polymers14,5091
Non-polymers4852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9943
Polymers14,5091
Non-polymers4852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9943
Polymers14,5091
Non-polymers4852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9943
Polymers14,5091
Non-polymers4852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9943
Polymers14,5091
Non-polymers4852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9943
Polymers14,5091
Non-polymers4852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9943
Polymers14,5091
Non-polymers4852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9943
Polymers14,5091
Non-polymers4852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.658, 75.081, 110.691
Angle α, β, γ (deg.)90.000, 94.380, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Fatty acid-binding protein, liver / Fatty acid-binding protein 1 / Liver-type fatty acid-binding protein / L-FABP


Mass: 14508.641 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP1, FABPL / Plasmid: PET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07148
#2: Chemical
ChemComp-VI9 / 2-({(3P)-4-cyclopropyl-5-methyl-3-[3-(trifluoromethyl)-1,2,4-oxadiazol-5-yl]thiophen-2-yl}carbamoyl)cyclopent-1-ene-1-carboxylic acid


Mass: 427.398 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C18H16F3N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 427 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein in 25mM Tris/HCl pH 7.5 100mM NaCl, see also PMID 27658368

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99988 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 2.21→42.53 Å / Num. obs: 46522 / % possible obs: 94.9 % / Redundancy: 3.12 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.57 / Num. measured all: 152972
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. possibleNum. unique obsNet I/σ(I) obs% possible all
2.21-2.240.440.56211354330.5938.1
2.24-2.291.450.55309725671.0382.9
2.29-2.343.040.507276526151.7194.6
2.34-2.393.420.454256624942.1897.2
2.39-2.443.40.398240223362.4997.3
2.44-2.53.320.361256924902.996.9
2.5-2.573.210.322272926293.2396.3
2.57-2.643.220.265244923774.1497.1
2.64-2.723.360.232251824635.0197.8
2.72-2.813.530.188244823966.4897.9
2.81-2.913.490.151242323748.0898
2.91-3.033.40.1232483243310.1998
3.03-3.173.220.0972447239712.3598
3.17-3.343.30.0762458240615.9397.9
3.34-3.553.460.0572419236921.0597.9
3.55-3.833.370.052417236423.9997.8
3.83-4.223.150.0432422234127.1696.7
4.22-4.853.260.0352454237431.4496.7
4.85-6.133.20.0342400232732.0297
6.13-42.533.180.0312410233734.8297

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
BUSTER2.11.2refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 2.23→42.53 Å / Cor.coef. Fo:Fc: 0.9596 / Cor.coef. Fo:Fc free: 0.9343 / SU R Cruickshank DPI: 0.375 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.377 / SU Rfree Blow DPI: 0.232 / SU Rfree Cruickshank DPI: 0.235
RfactorNum. reflection% reflectionSelection details
Rfree0.2427 2348 5.05 %RANDOM
Rwork0.1963 ---
obs0.1986 46486 97.11 %-
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 154.66 Å2 / Biso mean: 57.36 Å2 / Biso min: 26.39 Å2
Baniso -1Baniso -2Baniso -3
1--2.1465 Å20 Å2-2.9346 Å2
2---1.8976 Å20 Å2
3---4.0441 Å2
Refine analyzeLuzzati coordinate error obs: 0.433 Å
Refinement stepCycle: final / Resolution: 2.23→42.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7961 0 256 427 8644
Biso mean--67.76 52.06 -
Num. residues----1017
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3096SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes248HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1147HARMONIC5
X-RAY DIFFRACTIONt_it8315HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1120SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8960SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8315HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg11160HARMONIC21.3
X-RAY DIFFRACTIONt_omega_torsion3.54
X-RAY DIFFRACTIONt_other_torsion18.44
LS refinement shellResolution: 2.23→2.29 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4508 166 5.53 %
Rwork0.4841 2834 -
all0.4821 3000 -
obs--97.11 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.927-1.82310.67823.9867-0.97592.96390.03150.1141-0.00360.1743-0.0635-0.0577-0.1957-0.0390.032-0.01360.00510.0424-0.0777-0.0416-0.0574-6.798613.1939-38.3957
22.8199-1.3105-1.26113.1393-1.74654.0184-0.1274-0.34130.08770.26530.277-0.2832-0.17670.0675-0.14950.0101-0.0407-0.0529-0.0989-0.0783-0.0622-2.249514.4794-31.9006
31.5487-2.01971.600302.06715.0908-0.0088-0.21640.3515-0.40320.2541-0.3888-0.52070.2024-0.24530.0798-0.0030.0984-0.1298-0.03880.0068-0.455822.7796-37.3955
4-0.03041.45240.01191.5126-2.80024.87930.0564-0.09280.1246-0.28380.0368-0.2896-0.32390.0155-0.09320.12050.00340.0958-0.01650.03540.26287.659520.3992-41.2962
52.3561-0.9283-1.48382.1216-0.94721.24290.13640.36070.1218-0.1996-0.2527-0.5032-0.4743-0.35670.11640.0388-0.09020.1404-0.17360.00360.01095.009219.7437-47.8778
67.8511-2.52920.78633.4364-0.9840.32710.02120.51360.1664-0.4411-0.0926-0.3364-0.10020.05360.07150.0480.01280.0394-0.0414-0.0698-0.0684-3.89913.4039-46.1366
75.5879-1.7223-0.53800.66342.5282-0.09180.1824-0.2603-0.37030.1332-0.0732-0.10950.0008-0.0414-0.0038-0.02960.0386-0.0501-0.01890.0475-8.0410.1363-39.4507
86.7948-0.1915-2.47171.8225-2.76086.0731-0.0522-0.4166-0.56980.2305-0.18660.0782-0.00710.49690.2388-0.0356-0.00070.0207-0.1146-0.03220.030720.6088-6.9723-47.8559
98.15251.41090.27342.5666-0.93015.17720.304-0.0914-0.47220.1072-0.17130.2319-0.47230.5388-0.1326-0.0665-0.05660.0052-0.06650.0094-0.189722.6397-1.9471-51.6523
100.49070.6923-2.445601.6170.74490.1976-0.5717-0.11340.3258-0.39630.4508-0.53910.4840.19870.087-0.1576-0.01830.18890.0675-0.182929.07292.425-45.1684
111.99772.375-0.08110.0229-0.88280.49170.0131-0.2880.16140.0059-0.0986-0.035-0.02170.04680.08550.2416-0.1460.07520.1558-0.0842-0.290126.3659.4986-37.3679
128.3496-1.2314-2.51310.66472.78642.95920.0543-0.5830.46920.1038-0.023-0.1063-0.33460.4847-0.03130.1208-0.14850.0316-0.0434-0.0515-0.1322.57544.6273-38.139
134.41922.4759-2.24110-2.28883.1420.2621-0.5692-0.46760.3637-0.33890.3371-0.49430.50170.0768-0.0782-0.05360.03790.00380.0825-0.079319.9064-3.6834-38.5858
140.1111-1.7157-0.71958.2144-0.84956.35210.059-0.1534-0.25170.1707-0.2735-0.10060.28960.12540.2145-0.0085-0.00060.0676-0.20220.07410.151219.4972-8.9845-44.7033
151.6045-1.5104-0.16022.5402-0.36482.96580.0260.02150.08270.3777-0.3623-0.3732-0.21950.44680.3363-0.0549-0.0421-0.03750.03060.0567-0.049838.93911.2287-61.0757
163.0166-2.21211.03461.55381.22190.1413-0.0166-0.08430.07910.3293-0.0692-0.1236-0.1112-0.04910.08580.0935-0.0143-0.0492-0.0795-0.0215-0.012931.878813.6014-58.5179
171.8594-1.1479-1.57015.71362.8317.7006-0.04720.0063-0.2174-0.259-0.14320.0518-0.06870.05090.1904-0.09690.00490.0442-0.0274-0.013-0.033231.0427-6.7714-63.6896
180.0916-2.499-0.29314.09192.69644.89250.10620.1671-0.2609-0.0332-0.39730.41430.1017-0.08470.2911-0.01420.05210.02010.0592-0.0324-0.050528.4691-2.4321-74.6617
191.6268-0.38111.7312.8559-2.90952.3677-0.029-0.0621-0.4826-0.3725-0.0855-0.25760.17330.37470.11450.00530.08520.03580.15070.0390.005739.9391-3.6026-73.1144
201.3631-2.29371.10080.2557-1.1384.19390.11720.0404-0.3271-0.0982-0.2695-0.4070.09880.29960.1523-0.061-0.0051-0.00110.07040.0436-0.010942.4773-0.6399-64.0505
216.2292-2.9143-2.43761.30420.1991.9624-0.12610.06820.38040.33230.34470.1845-0.30710.0562-0.2185-0.04-0.03340.0383-0.0507-0.0583-0.1687-14.126527.4205-19.9198
226.27642.69712.45242.19812.89654.68260.1092-0.25160.07450.0968-0.216-0.13650.08360.51820.1068-0.1573-0.13990.01350.2849-0.16310.02298.910127.4808-20.975
233.1666-2.167-3.28132.92742.7537.53450.0250.1981-0.29360.5025-0.16560.39850.27210.03480.1407-0.1179-0.0150.0892-0.1146-0.0638-0.0732-9.71721.063-19.7592
240.3824-3.1192-1.16854.32782.680.1641-0.0367-0.0197-0.04940.51680.08330.12390.03440.1862-0.0466-0.07130.02980.0041-0.0116-0.0583-0.077-4.986716.8489-17.3135
251.22030.17521.20242.0782.79493.7449-0.0159-0.1652-0.21920.4960.1452-0.12890.25470.5326-0.12930.11970.128-0.02870.24740.0671-0.1758-4.225617.8352-7.7097
262.1047-0.082-0.57973.0151.03438.23870.1598-0.57340.10470.54120.2715-0.2316-0.43180.4843-0.4312-0.0489-0.0430.0126-0.0223-0.1359-0.0612-7.815329.1243-11.0686
276.6013-0.0576-2.88654.5351.31275.84470.066-0.18350.4912-0.13980.1994-0.4833-0.40380.359-0.26540.0195-0.06830.1166-0.1048-0.12360.028-5.350632.2222-18.7372
283.07921.0337-1.45412.71552.3408-0.09110.00270.389-0.07970.39370.08710.13020.5501-0.0859-0.08980.1164-0.14790.0117-0.1697-0.0361-0.0757-13.1956-18.9448-19.7298
290.28212.28511.61992.43640.50.9512-0.01390.0372-0.01730.09230.1458-0.06520.03450.0227-0.1319-0.04330.0118-0.0558-0.0907-0.05850.02680.2791-6.6376-21.5071
304.21170.356-0.10440.364-2.2816-0.035-0.06180.10980.2226-0.18230.2573-0.16440.21970.3581-0.1955-0.00310.00020.0634-0.0622-0.0919-0.01984.1072-9.8112-28.5036
310.7715-2.83482.89454.708-1.07940.4987-0.0801-0.2716-0.16220.52360.0629-0.0560.5303-0.09130.01720.2971-0.08090.0198-0.26360.0135-0.2171-8.7738-22.9368-20.1193
320.64492.7881-2.29685.3014-0.0946-0.3383-0.06090.1604-0.3490.55810.0923-0.16040.4550.1639-0.03140.22680.0455-0.037-0.3040.0196-0.1957-2.5085-25.364-18.0054
331.15131.28942.08840.8776-2.82020.3663-0.0071-0.0626-0.18260.2910.1805-0.08950.25770.14-0.17340.32540.1541-0.135-0.2143-0.07010.08164.8634-23.1575-12.7256
341.6649-2.46841.58130.0004-3.1082.43440.0254-0.1753-0.12450.37140.0387-0.34740.1345-0.1812-0.06410.3110.1326-0.1083-0.2207-0.068-0.2791.0361-22.4048-6.6898
354.06312.88322.24387.98360.19862.16040.0684-0.4688-0.25120.55350.1234-0.25710.56590.001-0.19180.13750.01840.0247-0.0753-0.0567-0.1401-7.1782-15.9698-10.1065
363.9902-1.31460.70240.0011.24712.7614-0.2095-0.3542-0.01360.28730.0875-0.06790.5131-0.2180.1220.0636-0.03960.0194-0.0298-0.0387-0.0378-10.022-12.5803-17.4539
378.2197-0.5656-0.9011.1859-0.00833.1746-0.1169-0.06750.5299-0.11940.01420.1398-0.1273-0.12550.1027-0.0120.0523-0.0025-0.0077-0.0109-0.028717.62434.1047-5.1207
386.3497-0.6783-0.94772.3468-0.39922.4602-0.0303-0.5105-0.1960.19010.08890.3456-0.0026-0.2407-0.0586-0.06450.04980.08640.04580.0127-0.120818.9434-0.7831-0.9204
391.01870.21770.886200.90984.7510.03270.1252-0.435-0.1410.09170.10450.28580.1765-0.1243-0.0580.09990.05770.09520.0084-0.142226.0075-5.6354-6.1315
400.995-2.6832.18893.20382.71341.18950.00530.1164-0.3211-0.26610.08470.20340.22170.0227-0.08990.12220.04640.0965-0.0802-0.04030.180520.8057-12.3774-9.86
41-0.42430.85772.76632.83150.76080.4274-0.02920.3973-0.2415-0.0356-0.10020.2652-0.06440.18680.12950.020.10240.0035-0.1274-0.0598-0.0321.3366-11.3253-15.4955
422.9402-0.62112.42333.57331.3122.76110.1670.4327-0.0799-0.4744-0.33310.3644-0.17790.53350.16610.04230.0756-0.04090.0508-0.0119-0.122619.15-1.3267-16.8571
43-0.0766-1.67981.95112.67661.25614.40760.05080.52370.4217-0.5046-0.2386-0.3975-0.52830.22250.1878-0.04120.03670.0086-0.01680.06470.036117.63265.3924-9.9681
442.9542-0.6567-0.1732.1552-1.88852.6258-0.16260.3353-0.0925-0.0653-0.0808-0.28830.39220.57150.2434-0.07390.14770.05050.18730.0616-0.166433.8705-2.585911.4122
452.0069-0.1134-0.316.7275-0.12641.89-0.0980.2954-0.2039-0.4751-0.0953-0.23180.43880.56720.1933-0.01530.11140.02690.06780.026-0.139527.9439-4.63358.9785
46-0.37322.46082.352.50083.0232.2596-0.1034-0.07520.38570.04550.02710.03520.2685-0.11330.07630.02520.0768-0.01550.0270.0091-0.082123.2843.642813.4765
476.23142.86190.87364.5279-0.16944.1728-0.0583-0.16470.3886-0.11720.01480.19940.1484-0.09920.0435-0.02680.09540.0010.00260.0044-0.13821.12120.523922.6847
486.31621.8528-1.45196.0754-2.46945.582-0.03490.48060.51060.3271-0.0727-0.5162-0.2210.58270.1077-0.12390.0861-0.03630.16270.0615-0.074133.98061.139720.8432
494.92640.5134-0.02110.00422.47837.7789-0.06920.24910.00330.2920.1911-0.19690.33520.3925-0.1219-0.22470.14720.02790.2190.0681-0.185536.9038-2.519913.1865
50-0.4276-2.32232.71050.9552-1.37242.1108-0.03520.1529-0.26520.2758-0.07730.16270.22320.05220.11250.0478-0.0312-0.0005-0.26830.04760.2812-10.7923-30.4777-35.4334
510.0879-0.7582-0.6020.2621-0.65770.7448-0.0006-0.06820.0287-0.0386-0.0511-0.0510.08080.00020.0517-0.18040.157-0.1691-0.0921-0.05990.22747.2083-34.513-35.5852
522.9359-2.74460.06860.5693-0.90610.2335-0.012-0.0459-0.02120.00570.02290.0013-0.01140.032-0.011-0.01020.1335-0.16980.0195-0.09370.1989.7849-29.06-29.5278
534.85451.2904-2.4422.4361.32284.6138-0.0208-0.0016-0.18690.1741-0.15070.11520.1552-0.13820.1715-0.0204-0.0396-0.064-0.2908-0.05110.0047-9.0001-24.9292-36.0797
543.3546-2.8995-2.62532.44081.1845.34530.0428-0.1308-0.08610.0735-0.0138-0.0350.16920.359-0.0290.0517-0.0075-0.0537-0.1386-0.01160.0992-5.1606-19.9912-39.2926
555.8923-2.4863-1.86411.1504-1.89513.77310.0477-0.04090.0281-0.14620.0564-0.1891-0.05450.1373-0.1041-0.19620.0599-0.06230.3035-0.0722-0.1881.5082-19.0347-45.6645
562.13280.0205-2.62050.10780.266-0.26310.01570.04380.0462-0.1035-0.0835-0.0844-0.00740.17870.0678-0.17370.1616-0.14890.1794-0.1199-0.2319-1.0467-20.9176-50.4561
570.8485-0.0871-2.80298.30272.36487.3185-0.02590.4460.0438-0.2168-0.06320.16090.40830.37950.0891-0.04910.0043-0.1785-0.2567-0.15210.2717-5.0558-30.1175-48.2824
581.48353.10842.21798.1796-2.50385.25040.10520.2255-0.27920.12950.07820.3580.56210.4688-0.18330.02630.0213-0.1625-0.3026-0.11130.279-5.6868-34.32-39.4268
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|-1 - A|21 }A-1 - 0
2X-RAY DIFFRACTION2{ A|22 - A|46 }A22 - 0
3X-RAY DIFFRACTION3{ A|47 - A|64 }A47 - 0
4X-RAY DIFFRACTION4{ A|65 - A|77 }A65 - 0
5X-RAY DIFFRACTION5{ A|78 - A|86 }A78 - 0
6X-RAY DIFFRACTION6{ A|87 - A|115 }A87 - 115
7X-RAY DIFFRACTION7{ A|116 - A|127 }A116 - 127
8X-RAY DIFFRACTION8{ B|2 - B|21 }B2 - 0
9X-RAY DIFFRACTION9{ B|22 - B|46 }B22 - 0
10X-RAY DIFFRACTION10{ B|47 - B|64 }B47 - 0
11X-RAY DIFFRACTION11{ B|65 - B|72 }B65 - 0
12X-RAY DIFFRACTION12{ B|73 - B|89 }B73 - 0
13X-RAY DIFFRACTION13{ B|90 - B|115 }B90 - 115
14X-RAY DIFFRACTION14{ B|116 - B|127 }B116 - 127
15X-RAY DIFFRACTION15{ C|2 - C|21 }C2 - 0
16X-RAY DIFFRACTION16{ C|22 - C|33 }C22 - 0
17X-RAY DIFFRACTION17{ C|34 - C|64 }C34 - 0
18X-RAY DIFFRACTION18{ C|65 - C|85 }C65 - 0
19X-RAY DIFFRACTION19{ C|86 - C|105 }C86 - 105
20X-RAY DIFFRACTION20{ C|106 - C|127 }C106 - 127
21X-RAY DIFFRACTION21{ D|-2 - D|13 }D-2 - 0
22X-RAY DIFFRACTION22{ D|14 - D|32 }D14 - 0
23X-RAY DIFFRACTION23{ D|33 - D|54 }D33 - 0
24X-RAY DIFFRACTION24{ D|55 - D|64 }D55 - 0
25X-RAY DIFFRACTION25{ D|65 - D|86 }D65 - 0
26X-RAY DIFFRACTION26{ D|87 - D|115 }D87 - 115
27X-RAY DIFFRACTION27{ D|116 - D|127 }D116 - 127
28X-RAY DIFFRACTION28{ E|2 - E|13 }E2 - 0
29X-RAY DIFFRACTION29{ E|14 - E|21 }E14 - 0
30X-RAY DIFFRACTION30{ E|22 - E|32 }E22 - 0
31X-RAY DIFFRACTION31{ E|33 - E|46 }E33 - 0
32X-RAY DIFFRACTION32{ E|47 - E|64 }E47 - 0
33X-RAY DIFFRACTION33{ E|65 - E|77 }E65 - 0
34X-RAY DIFFRACTION34{ E|78 - E|86 }E78 - 0
35X-RAY DIFFRACTION35{ E|87 - E|115 }E87 - 115
36X-RAY DIFFRACTION36{ E|116 - E|127 }E116 - 127
37X-RAY DIFFRACTION37{ F|2 - F|21 }F2 - 0
38X-RAY DIFFRACTION38{ F|22 - F|46 }F22 - 0
39X-RAY DIFFRACTION39{ F|47 - F|64 }F47 - 0
40X-RAY DIFFRACTION40{ F|65 - F|77 }F65 - 0
41X-RAY DIFFRACTION41{ F|78 - F|85 }F78 - 0
42X-RAY DIFFRACTION42{ F|86 - F|105 }F86 - 105
43X-RAY DIFFRACTION43{ F|106 - F|127 }F106 - 127
44X-RAY DIFFRACTION44{ G|1 - G|21 }G1 - 0
45X-RAY DIFFRACTION45{ G|22 - G|46 }G22 - 0
46X-RAY DIFFRACTION46{ G|47 - G|64 }G47 - 0
47X-RAY DIFFRACTION47{ G|65 - G|85 }G65 - 0
48X-RAY DIFFRACTION48{ G|86 - G|115 }G86 - 115
49X-RAY DIFFRACTION49{ G|116 - G|127 }G116 - 127
50X-RAY DIFFRACTION50{ H|2 - H|13 }H2 - 0
51X-RAY DIFFRACTION51{ H|14 - H|21 }H14 - 0
52X-RAY DIFFRACTION52{ H|22 - H|32 }H22 - 0
53X-RAY DIFFRACTION53{ H|33 - H|46 }H33 - 0
54X-RAY DIFFRACTION54{ H|47 - H|64 }H47 - 0
55X-RAY DIFFRACTION55{ H|65 - H|77 }H65 - 0
56X-RAY DIFFRACTION56{ H|78 - H|85 }H78 - 0
57X-RAY DIFFRACTION57{ H|86 - H|105 }H86 - 105
58X-RAY DIFFRACTION58{ H|106 - H|127 }H106 - 127

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more