4I0P
HLA-DO in complex with HLA-DM
- PDB DOI: https://doi.org/10.2210/pdb4I0P/pdb
- Entry: 4I0P supersedes: 3USA
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Drosophila melanogaster
- Mutation(s): No 
- Deposited: 2012-11-18 Released: 2012-12-26 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.20 Å
- R-Value Free: 0.242 
- R-Value Work: 0.188 
- R-Value Observed: 0.191 
This is version 1.3 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-DMA protein | 188 | Homo sapiens | Mutation(s): 0  Gene Names: 3108, HLA-DMA | ||
UniProt | |||||
Find proteins for Q6ICR9 (Homo sapiens) Explore Q6ICR9  Go to UniProtKB:  Q6ICR9 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q6ICR9 | ||||
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, DM beta chain | 191 | Homo sapiens | Mutation(s): 0  Gene Names: 3109, DMB, HLA-DMB, RING7 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P28068 (Homo sapiens) Explore P28068  Go to UniProtKB:  P28068 | |||||
PHAROS:  P28068 GTEx:  ENSG00000242574  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P28068 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
HLA class II histocompatibility antigen, DO alpha chain | 181 | Homo sapiens | Mutation(s): 0  Gene Names: 3111, HLA-DNA, HLA-DOA, HLA-DZA | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P06340 (Homo sapiens) Explore P06340  Go to UniProtKB:  P06340 | |||||
PHAROS:  P06340 GTEx:  ENSG00000204252  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P06340 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
HLA class II histocompatibility antigen, DO beta chain | 189 | Homo sapiens | Mutation(s): 0  Gene Names: 3112, HLA-DOB | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P13765 (Homo sapiens) Explore P13765  Go to UniProtKB:  P13765 | |||||
PHAROS:  P13765 GTEx:  ENSG00000241106  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P13765 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | I [auth A] J [auth C] K [auth D] M [auth E] O [auth G] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
PGE Query on PGE | R [auth H] | TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N | |||
GOL Query on GOL | L [auth D], N [auth F], T [auth H] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
ACT Query on ACT | S [auth H] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.20 Å
- R-Value Free: 0.242 
- R-Value Work: 0.188 
- R-Value Observed: 0.191 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 83.26 | α = 90 |
b = 147.1 | β = 106.49 |
c = 95.959 | γ = 90 |
Software Name | Purpose |
---|---|
HKL-2000 | data collection |
PHASER | phasing |
PHENIX | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
Entry History 
Deposition Data
- Released Date: 2012-12-26  Deposition Author(s): Guce, A.I., Mortimer, S.E., Stern, L.J.
- This entry supersedes: 3USA
Revision History (Full details and data files)
- Version 1.0: 2012-12-26
Type: Initial release - Version 1.1: 2013-01-16
Changes: Database references - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.3: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary