Research workbench
Crystal structure of INHA:01 TCR in complex with HLA-E (Y84C) bound to inha (53-61 gcg)
Analyse Crystal structure of INHA:01 TCR in complex with HLA-E (Y84C) bound to inha… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZKX
- Type
- protein
- Length
- 821 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, alpha chain E; Beta-2-microglobulin…
- EC
- 1.3.1.9
- UniProt
- P13747, P61769, P9WGR1
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, alpha chain E | protein | 274 | 23% helix, 41% strand | P13747 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 12 | 0% helix, 25% strand | P9WGR1 |
| D | T-cell receptor alpha chain | protein | 190 | 3% helix, 49% strand | — |
| E | T-cell receptor beta chain | protein | 245 | 7% helix, 49% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 669 | 0.71 | 0.78 | 55 | EDO |
| 2 | 961 | 0.70 | 0.75 | 73 | EDO |
| 3 | 155 | 0.55 | 0.81 | 19 | empty |
| 4 | 166 | 0.49 | 0.78 | 23 | empty |
| 5 | 124 | 0.49 | 0.80 | 17 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2250 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1375 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1143 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 662 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 392 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 6ZKX · Crystal structure of InhA:01 TCR in complex with HLA-E (Y84C) bound to InhA (53-61 GCG) · the same entry in another collection · chain E against E, 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 0.99
- P13747 · AlphaFold monomer V2.0 prediction for HLA class I histocompatibility antigen, alpha chain… · a predicted model of the same protein · chain A against A, TM-score 0.93
- P9WGR1 · AlphaFold monomer V2.0 prediction for enoyl-[acyl-carrier-protein] reductase [NADH]… · a predicted model of the same protein · chain C against A, TM-score 0.29
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 P13747
- Every structure of UniProt P61769
- Every structure of UniProt P9WGR1
- Elsewhere: RCSB PDB 6ZKX · PDBe 6ZKX · UniProt P13747 · UniProt P61769 · UniProt P9WGR1
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