MolNFT v1 · #171921 · protein
Crystal structure of INHA:01 TCR in complex with HLA-E (F116C) bound to inha (53-61 H4C)
6ZKZ · HLA class I histocompatibility antigen, alpha chain E: “Crystal structure of INHA:01 TCR in complex with HLA-E (F116C) bound to inha (53-61 H4C)”. X-ray diffraction, 1 ligand (QM8), 11 pockets (best druggability 0.71). MolNFT v1…
- PDB
- 6ZKZ
- Type
- protein
- Length
- 812 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
- Ligands
- QM8
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, alpha chain E | protein | 272 | 26% helix, 39% 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 | 8 | 0% helix, 0% strand | P9WGR1 |
| D | T-cell receptor alpha chain | protein | 189 | 3% helix, 50% strand | — |
| E | T-cell receptor beta chain | protein | 243 | 7% helix, 50% strand | — |
Ligands and binding sites
- QM8 · 6-sulfanyl-L-norleucine · ligand · chains A, C
- EDO · 1,2-ethanediol · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.71 | 0.75 | 75 | EDO |
| 2 | 620 | 0.68 | 0.77 | 54 | EDO |
| 3 | 138 | 0.51 | 0.80 | 18 | empty |
| 4 | 109 | 0.49 | 0.81 | 17 | empty |
| 5 | 180 | 0.48 | 0.76 | 32 | EDO |
Interfaces
7 interfaces between chains.
- D–E · 2276 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1414 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 838 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 521 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 412 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 6ZKZ · Crystal structure of InhA:01 TCR in complex with HLA-E (F116C) bound to InhA (53-61 H4C) · 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 0.94
- 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 0.45
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 6ZKZ · PDBe 6ZKZ · UniProt P13747 · UniProt P61769 · UniProt P9WGR1
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