MolNFT v1 · #147875 · protein
HLA class I histocompatibility antigen
6EQB · HLA class I histocompatibility antigen, a-2 alpha chain: “HLA class I histocompatibility antigen”. X-ray diffraction, 1 ligand (SO4), 12 pockets (best druggability 0.71). MolNFT v1 #147875 on GenesisL1: 3D structure, binding sites…
- PDB
- 6EQB
- Type
- protein
- Length
- 825 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin…
- UniProt
- P01892, P61769
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 276 | 25% helix, 34% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 48% strand | P61769 |
| C | Ala-ala-gly-ile-gly-ile-leu-thr-val | protein | 9 | 0% helix, 22% strand | — |
| D | High affinity MEL5 TCR, alpha chain | protein | 196 | 2% helix, 44% strand | — |
| E | High affinity MEL5 TCR, beta chain | protein | 244 | 7% helix, 52% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, E, B, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, E
- EDO · 1,2-ethanediol · additive · 2 copies · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1157 | 0.71 | 0.75 | 85 | EDO |
| 2 | 576 | 0.66 | 0.77 | 61 | empty |
| 3 | 64 | 0.62 | 0.91 | 17 | empty |
| 4 | 133 | 0.62 | 0.86 | 38 | empty |
| 5 | 106 | 0.56 | 0.85 | 18 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2203 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1396 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 751 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 566 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 561 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
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 P01892
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6EQB · PDBe 6EQB · UniProt P01892 · UniProt P61769
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