Research workbench
Crystal structure of HLA molecule with an kir receptor
Analyse Crystal structure of HLA molecule with an kir receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DUU
- Type
- protein
- Length
- 578 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Leu-asn-pro-ser-val-ala-ala-thr-leu; Killer…
- UniProt
- F6IQA6, P61769, P43631
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 273 | 27% helix, 38% strand | F6IQA6 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 47% strand | P61769 |
| C | Leu-asn-pro-ser-val-ala-ala-thr-leu | protein | 9 | 0% helix, 0% strand | — |
| D | Killer cell immunoglobulin-like receptor 2DS2 | protein | 196 | 2% helix, 55% strand | P43631 |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.66 | 0.76 | 54 | empty |
| 2 | 204 | 0.50 | 0.76 | 31 | empty |
| 3 | 76 | 0.49 | 0.83 | 17 | empty |
| 4 | 141 | 0.48 | 0.78 | 20 | empty |
| 5 | 53 | 0.44 | 0.84 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1323 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 839 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 654 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 52 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7DUU · Crystal structure of HLA molecule with an KIR receptor · the same entry in another collection · chain A against A, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P43631 · AlphaFold monomer V2.0 prediction for killer cell immunoglobulin-like receptor 2DS2… · a predicted model of the same protein · chain D against A, TM-score 0.95
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt F6IQA6
- Every structure of UniProt P61769
- Every structure of UniProt P43631
- Elsewhere: RCSB PDB 7DUU · PDBe 7DUU · UniProt F6IQA6 · UniProt P61769 · UniProt P43631
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