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- PDB-2j0g: L-ficolin complexed to N-acetyl-mannosamine -

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Basic information

Entry
Database: PDB / ID: 2j0g
TitleL-ficolin complexed to N-acetyl-mannosamine
ComponentsFICOLIN-2
KeywordsLECTIN / GLYCOPROTEIN / INNATE IMMUNITY / FIBRINOGEN-LIKE DOMAIN / COLLAGEN / IMMUNOLOGY / LECTIN-LIKE / PATTERN- RECOGNITION-PROTEIN
Function / homology
Function and homology information


mannan binding / recognition of apoptotic cell / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / positive regulation of opsonization / cell surface pattern recognition receptor signaling pathway / opsonization / complement activation, lectin pathway / carbohydrate derivative binding / collagen trimer ...mannan binding / recognition of apoptotic cell / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / positive regulation of opsonization / cell surface pattern recognition receptor signaling pathway / opsonization / complement activation, lectin pathway / carbohydrate derivative binding / collagen trimer / serine-type endopeptidase complex / proteoglycan binding / Initial triggering of complement / antigen binding / calcium-dependent protein binding / collagen-containing extracellular matrix / defense response to Gram-negative bacterium / blood microparticle / defense response to Gram-positive bacterium / external side of plasma membrane / signaling receptor binding / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding
Similarity search - Function
Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain ...Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Few Secondary Structures / Irregular / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-mannopyranose / alpha-D-mannopyranose / Ficolin-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.85 Å
AuthorsGarlatti, V. / Gaboriaud, C.
CitationJournal: Embo J. / Year: 2007
Title: Structural Insights Into the Innate Immune Recognition Specificities of L- and H-Ficolins.
Authors: Garlatti, V. / Belloy, N. / Martin, L. / Lacroix, M. / Matsushita, M. / Endo, Y. / Fujita, T. / Fontecilla-Camps, J.C. / Arlaud, G.J. / Thielens, N.M. / Gaboriaud, C.
History
DepositionAug 3, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Apr 3, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FICOLIN-2
B: FICOLIN-2
C: FICOLIN-2
D: FICOLIN-2
E: FICOLIN-2
F: FICOLIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,30919
Polymers148,3766
Non-polymers2,93313
Water82946
1
A: FICOLIN-2
B: FICOLIN-2
C: FICOLIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6459
Polymers74,1883
Non-polymers1,4576
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: FICOLIN-2
E: FICOLIN-2
F: FICOLIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,66310
Polymers74,1883
Non-polymers1,4757
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)96.940, 96.940, 139.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12C
22B
32E
42F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A79 - 84
2112B79 - 84
3112C79 - 84
4112D79 - 84
5112E79 - 84
6112F79 - 84
1212A87 - 96
2212B87 - 96
3212C87 - 96
4212D87 - 96
5212E87 - 96
6212F87 - 96
1312A106 - 121
2312B106 - 121
3312C106 - 121
4312D106 - 121
5312E106 - 121
6312F106 - 121
1412A123 - 157
2412B123 - 157
3412C123 - 157
4412D123 - 157
5412E123 - 157
6412F123 - 157
1512A184 - 191
2512B184 - 191
3512C184 - 191
4512D184 - 191
5512E184 - 191
6512F184 - 191
1612A248 - 271
2612B248 - 271
3612C248 - 271
4612D248 - 271
5612E248 - 271
6612F248 - 271
1712A273 - 286
2712B273 - 286
3712C273 - 286
4712D273 - 286
5712E273 - 286
6712F273 - 286
1122C224 - 231
2122B224 - 231
3122E224 - 231
4122F224 - 231

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
FICOLIN-2 / COLLAGEN/FIBRINOGEN DOMAIN-CONTAINING PROTEIN 2 / L-FICOLIN / FICOLIN-B / SERUM LECTIN P35 / EBP-37 / HUCOLIN


Mass: 24729.318 Da / Num. of mol.: 6 / Fragment: BINDING DOMAIN, RESIDUES 97-313
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: PLASMA / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q15485

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Sugars , 4 types, 7 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-2-3/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-Manp]{[(2+?)][]{[(?+2)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-Manp]{[(2+?)][]{[(?+2)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-BM3 / 2-acetamido-2-deoxy-alpha-D-mannopyranose


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DManpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-mannopyranosamineCOMMON NAMEGMML 1.0
a-D-ManpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar ChemComp-MAN / alpha-D-mannopyranose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 52 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsC-TERMINAL DOMAIN CONFLICTS BETWEEN UNP SEQUENCE AND COORDINATES: THERE IS A DIFFERENCE BECAUSE ...C-TERMINAL DOMAIN CONFLICTS BETWEEN UNP SEQUENCE AND COORDINATES: THERE IS A DIFFERENCE BECAUSE POINTS OF POLYMORPHISM EXIST IN L FICOLIN FOR 247 AND 168. THE CDNA USED CORRESPONDS TO ONE WIDESPREAD ALLELE AND THE SEQUENCE IN UNP TO ANOTHER

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.47 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 21, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 33923 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.6

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.85→15 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.894 / SU B: 35.37 / SU ML: 0.322 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.414 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1681 5 %RANDOM
Rwork0.193 ---
obs0.196 31942 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å2-0.3 Å20 Å2
2---0.61 Å20 Å2
3---0.91 Å2
Refinement stepCycle: LAST / Resolution: 2.85→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10328 0 186 46 10560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02110819
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.92714663
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20251287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.76823.644579
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.408151645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5521573
X-RAY DIFFRACTIONr_chiral_restr0.0980.21487
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028499
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2520.34755
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3360.57095
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.5699
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2940.344
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2630.511
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.59626446
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.998310088
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.06635057
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5844575
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A448tight positional00.05
12B448tight positional00.05
13C448tight positional00.05
14D448tight positional00.05
15E448tight positional00.05
16F448tight positional00.05
21C32tight positional00.05
22B32tight positional00.05
23E32tight positional00.05
24F32tight positional00.05
11A443medium positional0.10.5
12B443medium positional0.110.5
13C443medium positional0.110.5
14D443medium positional0.10.5
15E443medium positional0.110.5
16F443medium positional0.10.5
21C27medium positional0.120.5
22B27medium positional0.110.5
23E27medium positional0.120.5
24F27medium positional0.10.5
11A448tight thermal00.5
12B448tight thermal00.5
13C448tight thermal00.5
14D448tight thermal00.5
15E448tight thermal00.5
16F448tight thermal00.5
21C32tight thermal00.5
22B32tight thermal00.5
23E32tight thermal00.5
24F32tight thermal00.5
11A443medium thermal0.052
12B443medium thermal0.062
13C443medium thermal0.062
14D443medium thermal0.052
15E443medium thermal0.052
16F443medium thermal0.052
21C27medium thermal0.052
22B27medium thermal0.062
23E27medium thermal0.062
24F27medium thermal0.062
LS refinement shellResolution: 2.85→2.95 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.384 163
Rwork0.31 3089
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)
14.31530.21330.14111.9207-0.75832.29860.0017-0.2499-0.74080.0989-0.06610.18720.0080.16850.06440.1580.0920.0744-0.09220.0750.136846.86839.6434.418
21.4883-0.4868-0.1042.9459-0.04181.91730.14080.11960.3362-0.09250.0126-0.1939-0.40310.1477-0.1534-0.0824-0.00370.0683-0.14120.0407-0.065763.36327.5975.243
31.0656-0.0982-0.02693.4546-2.12253.9585-0.0447-0.222-0.02720.83110.18480.57-0.4848-0.3148-0.14010.04920.02580.0855-0.10180.0378-0.045756.49745.2321.243
42.4679-0.55871.19243.53330.96092.6306-0.05070.2381-0.6011-0.2323-0.04670.3561-0.24510.01130.0974-0.0836-0.0630.00460.2051-0.14780.142410.9174.44515.589
53.5670.5451-0.02411.66670.34631.7102-0.0026-0.18030.22460.03580.247-0.5159-0.25240.6061-0.2445-0.1123-0.0575-0.01490.0861-0.16630.04431.55210.9215.131
63.28811.02662.07521.35631.2023.8747-0.09710.9007-0.6227-0.22470.3068-0.256-0.03350.589-0.2097-0.086-0.05910.01190.0898-0.1498-0.005110.88815.62818.795
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A76 - 287
2X-RAY DIFFRACTION2B75 - 288
3X-RAY DIFFRACTION3C75 - 288
4X-RAY DIFFRACTION4D75 - 288
5X-RAY DIFFRACTION5E75 - 288
6X-RAY DIFFRACTION6F77 - 288

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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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