6BIJ
HLA-DRB1 in complex with citrullinated fibrinogen peptide
- PDB DOI: https://doi.org/10.2210/pdb6BIJ/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2017-11-02 Released: 2018-01-17 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.239 
- R-Value Work: 0.181 
- R-Value Observed: 0.184 
This is version 2.0 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
HLA class II histocompatibility antigen, DR alpha chain | 177 | Homo sapiens | Mutation(s): 0  Gene Names: HLA-DRA, HLA-DRA1 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01903 (Homo sapiens) Explore P01903  Go to UniProtKB:  P01903 | |||||
PHAROS:  P01903 GTEx:  ENSG00000204287  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P01903 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
HLA class II histocompatibility antigen, DRB1-4 beta chain | 189 | Homo sapiens | Mutation(s): 0  Gene Names: HLA-DRB1 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01911 (Homo sapiens) Explore P01911  Go to UniProtKB:  P01911 | |||||
PHAROS:  P01911 GTEx:  ENSG00000196126  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P01911 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Citrullinated Fibrinogen 72,74Cit69-81 | 13 | Homo sapiens | Mutation(s): 0  | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P02675 (Homo sapiens) Explore P02675  Go to UniProtKB:  P02675 | |||||
PHAROS:  P02675 GTEx:  ENSG00000171564  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P02675 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | D [auth A], E [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
CIR Query on CIR | C | L-PEPTIDE LINKING | C6 H13 N3 O3 | ARG |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.239 
- R-Value Work: 0.181 
- R-Value Observed: 0.184 
- Space Group: C 2 2 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 67.01 | α = 90 |
b = 177.71 | β = 90 |
c = 77.04 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2018-01-17  Deposition Author(s): Ting, Y.T., Scally, S.W., Rossjohn, J.
Revision History (Full details and data files)
- Version 1.0: 2018-01-17
Type: Initial release - Version 1.1: 2018-01-24
Changes: Database references, Structure summary - Version 1.2: 2018-03-14
Changes: Advisory, Database references - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.4: 2022-04-27
Changes: Advisory, Database references, Structure summary - Version 1.5: 2023-10-04
Changes: Data collection, Refinement description - Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Derived calculations