MolNFT v1 · #147874 · protein
HLA class I histocompatibility antigen
6EQA · HLA class I histocompatibility antigen, a-2 alpha chain: “HLA class I histocompatibility antigen”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.69). MolNFT v1 #147874 on GenesisL1: 3D structure, binding sites…
- PDB
- 6EQA
- Type
- protein
- Length
- 823 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
- 11 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 276 | 26% helix, 37% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Ala-ala-gly-ile-gly-ile-leu-thr-val | protein | 9 | 0% helix, 11% strand | — |
| D | MEL5 TCR, alpha chain | protein | 194 | 2% helix, 48% strand | — |
| E | MEL5 TCR, beta chain | protein | 244 | 7% helix, 52% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.69 | 0.74 | 78 | SO4 |
| 2 | 636 | 0.69 | 0.77 | 61 | empty |
| 3 | 249 | 0.65 | 0.83 | 43 | empty |
| 4 | 186 | 0.59 | 0.82 | 34 | empty |
| 5 | 125 | 0.47 | 0.79 | 24 | SO4 |
Interfaces
7 interfaces between chains.
- D–E · 2140 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1433 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 724 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 471 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 438 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 6EQA · PDBe 6EQA · UniProt P01892 · UniProt P61769
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