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- PDB-4cdc: Human DPP1 in complex with (2S)-2-amino-N-((1S)-1-cyano-2-(4- phe... -

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Basic information

Entry
Database: PDB / ID: 4cdc
TitleHuman DPP1 in complex with (2S)-2-amino-N-((1S)-1-cyano-2-(4- phenylphenyl)ethyl)butanamide
Components(DIPEPTIDYL PEPTIDASE 1 ...Cathepsin C) x 3
KeywordsHYDROLASE / INHIBITOR
Function / homology
Function and homology information


dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / negative regulation of myelination / positive regulation of microglial cell activation / Cargo concentration in the ER / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding / COPII-coated ER to Golgi transport vesicle ...dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / negative regulation of myelination / positive regulation of microglial cell activation / Cargo concentration in the ER / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding / COPII-coated ER to Golgi transport vesicle / phosphatase binding / cysteine-type peptidase activity / positive regulation of apoptotic signaling pathway / MHC class II antigen presentation / endoplasmic reticulum-Golgi intermediate compartment membrane / proteolysis involved in protein catabolic process / response to organic substance / T cell mediated cytotoxicity / : / azurophil granule lumen / protein-folding chaperone binding / collagen-containing extracellular matrix / lysosome / immune response / endoplasmic reticulum lumen / cysteine-type endopeptidase activity / serine-type endopeptidase activity / intracellular membrane-bounded organelle / centrosome / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / identical protein binding
Similarity search - Function
Cathepsin C, exclusion domain / Cysteine proteinases. Chain C / Cathepsin C exclusion / Cathepsin C, exclusion domain superfamily / Cathepsin C / Cathepsin C exclusion domain / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site ...Cathepsin C, exclusion domain / Cysteine proteinases. Chain C / Cathepsin C exclusion / Cathepsin C, exclusion domain superfamily / Cathepsin C / Cathepsin C exclusion domain / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Lipocalin / Papain-like cysteine peptidase superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-6AO / Dipeptidyl peptidase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDebreczeni, J. / Edman, K. / Furber, M. / Tiden, A. / Gardiner, P. / Mete, T. / Ford, R. / Millichip, I. / Stein, L. / Mather, A. ...Debreczeni, J. / Edman, K. / Furber, M. / Tiden, A. / Gardiner, P. / Mete, T. / Ford, R. / Millichip, I. / Stein, L. / Mather, A. / Kinchin, E. / Luckhurst, C. / Cage, P. / Sanghanee, H. / Breed, J. / Wissler, L.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Cathepsin C Inhibitors: Property Optimization and Identification of a Clinical Candidate.
Authors: Furber, M. / Gardiner, P. / Tiden, A.K. / Mete, A. / Ford, R. / Millichip, I. / Stein, L. / Mather, A. / Kinchin, E. / Luckhurst, C. / Barber, S. / Cage, P. / Sanganee, H. / Austin, R. / ...Authors: Furber, M. / Gardiner, P. / Tiden, A.K. / Mete, A. / Ford, R. / Millichip, I. / Stein, L. / Mather, A. / Kinchin, E. / Luckhurst, C. / Barber, S. / Cage, P. / Sanganee, H. / Austin, R. / Chohan, K. / Beri, R. / Thong, B. / Wallace, A. / Oreffo, V. / Hutchinson, R. / Harper, S. / Debreczeni, J. / Breed, J. / Wissler, L. / Edman, K.
History
DepositionOct 31, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Apr 24, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "JA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN
B: DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN
C: DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN
D: DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN
E: DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN
F: DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN
G: DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN
H: DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN
I: DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN
J: DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN
K: DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN
L: DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,15131
Polymers158,85512
Non-polymers3,29619
Water5,603311
1
G: DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN
H: DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN
I: DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6859
Polymers39,7143
Non-polymers9716
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9580 Å2
ΔGint-62.2 kcal/mol
Surface area15290 Å2
MethodPISA
2
D: DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN
E: DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN
F: DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3727
Polymers39,7143
Non-polymers6584
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9080 Å2
ΔGint-66.6 kcal/mol
Surface area15020 Å2
MethodPISA
3
A: DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN
B: DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN
C: DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5017
Polymers39,7143
Non-polymers7874
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9090 Å2
ΔGint-60.4 kcal/mol
Surface area15270 Å2
MethodPISA
4
J: DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN
K: DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN
L: DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5938
Polymers39,7143
Non-polymers8795
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9260 Å2
ΔGint-61.9 kcal/mol
Surface area15270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.276, 84.276, 224.626
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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DIPEPTIDYL PEPTIDASE 1 ... , 3 types, 12 molecules ADGJBEHKCFIL

#1: Protein
DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN / DIPEPTIDYL PEPTIDASE I EXCLUSION DOMAIN CHAIN / CATHEPSIN C / CATHEPSIN J / DIPEPTIDYL PEPTIDASE I ...DIPEPTIDYL PEPTIDASE I EXCLUSION DOMAIN CHAIN / CATHEPSIN C / CATHEPSIN J / DIPEPTIDYL PEPTIDASE I / DPP-I / DPPI / DIPEPTIDYL TRANSFERASE


Mass: 13500.163 Da / Num. of mol.: 4 / Fragment: DPP1 EXCLUSION DOMAIN, RESIDUES 25-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P53634, dipeptidyl-peptidase I
#2: Protein
DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN / Cathepsin C / DIPEPTIDYL PEPTIDASE I HEAVY CHAIN / CATHEPSIN C / CATHEPSIN J / DIPEPTIDYL PEPTIDASE I / DPP-I / ...DIPEPTIDYL PEPTIDASE I HEAVY CHAIN / CATHEPSIN C / CATHEPSIN J / DIPEPTIDYL PEPTIDASE I / DPP-I / DPPI / DIPEPTIDYL TRANSFERASE


Mass: 18630.018 Da / Num. of mol.: 4 / Fragment: DPP1 HEAVY CHAIN, RESIDUES 230-394
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P53634, dipeptidyl-peptidase I
#3: Protein
DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN / Cathepsin C / DIPEPTIDYL PEPTIDASE I LIGHT CHAIN / CATHEPSIN C / CATHEPSIN J / DIPEPTIDYL PEPTIDASE I / DPP-I / ...DIPEPTIDYL PEPTIDASE I LIGHT CHAIN / CATHEPSIN C / CATHEPSIN J / DIPEPTIDYL PEPTIDASE I / DPP-I / DPPI / DIPEPTIDYL TRANSFERASE


Mass: 7583.444 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P53634, dipeptidyl-peptidase I

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Sugars , 1 types, 7 molecules

#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 323 molecules

#5: Chemical
ChemComp-6AO / (2S)-2-azanyl-N-[(2S)-1-azanylidene-3-(4-phenylphenyl)propan-2-yl]butanamide


Mass: 309.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H23N3O
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsN-ACETYL-D-GLUCOSAMINE (NAG): POSTTRANSLATIONAL MODIFICATION

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.57 % / Description: NONE
Crystal growDetails: 21% PEG3350, 200MM AMSO4, 100MM NA ACETATE PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.4→75 Å / Num. obs: 67307 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 1.6 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 4.1
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.1 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K3B

1k3b


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.899 / SU B: 13.001 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.377 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2325 3397 5.1 %RANDOM
Rwork0.19068 ---
obs0.19278 63603 96.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.159 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.02 Å20 Å2
2--0.02 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10882 0 218 311 11411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01911460
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210162
X-RAY DIFFRACTIONr_angle_refined_deg1.1761.94215552
X-RAY DIFFRACTIONr_angle_other_deg0.7323.00423290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04151357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11923.85535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.489151697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2961540
X-RAY DIFFRACTIONr_chiral_restr0.070.21611
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213025
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022833
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5521.0675479
X-RAY DIFFRACTIONr_mcbond_other0.5521.0675478
X-RAY DIFFRACTIONr_mcangle_it0.991.7956819
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.8691.1745981
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 252 -
Rwork0.26 4551 -
obs--96.47 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3921-0.12540.22722.2721-0.73362.103-0.1498-0.05070.2808-0.02970.0166-0.0741-0.34220.11930.13320.1726-0.1449-0.01710.1694-0.04760.1874-10.644123.1849-0.705
21.52830.01470.22581.0480.30791.4012-0.02220.0069-0.1738-0.08320.0358-0.177-0.01830.2301-0.01360.0522-0.04510.02320.1923-0.04750.1969-2.2024-0.5192-3.1226
31.26690.34330.15391.73730.06462.20110.0759-0.1508-0.23810.1074-0.0324-0.20320.06970.1409-0.04360.0127-0.0157-0.00450.2227-0.01680.2343-3.6727-4.28386.698
43.84420.19651.19453.17980.24981.6171-0.03030.3646-0.3111-0.37030.0835-0.15620.09430.2366-0.05320.1927-0.07930.04490.2045-0.04910.0375-23.0908-0.8429-29.3387
51.6944-0.09160.4581.7630.31260.9203-0.08090.07050.2377-0.23320.04250.0133-0.22920.01590.03840.2336-0.116-0.07130.11420.0450.0957-34.450321.2307-23.9688
61.98810.62210.22831.91630.18680.7325-0.177-0.01720.1158-0.19310.09380.315-0.1454-0.06850.08330.2041-0.0401-0.0970.13070.04370.1321-44.179818.5221-22.9591
72.54070.17670.33661.41960.55271.9256-0.0618-0.16620.0408-0.0966-0.07490.249-0.0491-0.2760.13670.0489-0.0673-0.04070.21420.00680.1571-56.8634-3.4761-4.3837
81.33460.02570.1821.50850.32661.41220.0268-0.0648-0.25590.05820-0.04570.1741-0.1392-0.02680.1313-0.1238-0.04140.12040.05030.1991-40.5838-22.6671-1.9745
92.0028-0.1597-0.09931.53220.2191.05440.04140.1745-0.3259-0.1505-0.0066-0.15350.1409-0.1173-0.03480.1387-0.0988-0.01380.10070.00280.2233-36.5889-23.2687-11.7771
102.740.50060.68453.40870.75982.43740.0968-0.3684-0.25960.32940.0361-0.15430.3283-0.0792-0.1330.1381-0.0492-0.02150.25580.06130.0348-29.8478-4.868923.9915
111.92480.03350.57621.64770.59681.0608-0.0807-0.27230.15480.0613-0.00170.1851-0.1457-0.27270.08240.05280.02860.01310.2969-0.08420.0915-43.574215.872218.9637
122.3736-0.06220.49221.61410.30361.4895-0.1796-0.16540.35760.03910.101-0.0799-0.1842-0.10540.07860.10170.03-0.01490.2014-0.09980.1219-36.045923.218917.8789
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 119
2X-RAY DIFFRACTION2B206 - 367
3X-RAY DIFFRACTION3C372 - 439
4X-RAY DIFFRACTION4D1 - 118
5X-RAY DIFFRACTION5E206 - 367
6X-RAY DIFFRACTION6F372 - 439
7X-RAY DIFFRACTION7G1 - 119
8X-RAY DIFFRACTION8H206 - 367
9X-RAY DIFFRACTION9I372 - 439
10X-RAY DIFFRACTION10J1 - 119
11X-RAY DIFFRACTION11K206 - 367
12X-RAY DIFFRACTION12L372 - 439

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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

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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

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