MolNFT v1 · #167502 · protein
Structure of HD14 TCR in complex with HLA-B7 presenting an EBV epitope
6VMX · HLA class I histocompatibility antigen, B-7 alpha chain: “Structure of HD14 TCR in complex with HLA-B7 presenting an EBV epitope”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #167502 on GenesisL1: 3D structure…
- PDB
- 6VMX
- Type
- protein
- Length
- 1,652 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-7 alpha chain; Beta-2-microglobulin…
- UniProt
- P01889, P61769, P12977
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 7 distinct chains · 14% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-7 alpha chain | protein | 276 | 25% helix, 39% strand | P01889 |
| B, G | Beta-2-microglobulin | protein | 100 | 0% helix, 47% strand | P61769 |
| C, H | Epstein-barr nuclear antigen 3 | protein | 9 | 0% helix, 0% strand | P12977 |
| D, I | HD14 alpha chain | protein | 203 | 3% helix, 44% strand | — |
| E | HD14 beta chain | protein | 243 | 7% helix, 50% strand | — |
| F | HLA class I histocompatibility antigen, B-7 alpha chain | protein | 267 | 27% helix, 36% strand | P01889 |
| J | HD14 beta chain | protein | 242 | 7% helix, 51% strand | — |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, E, F, J
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, J, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.84 | 0.85 | 99 | empty |
| 2 | 918 | 0.74 | 0.78 | 76 | empty |
| 3 | 1190 | 0.72 | 0.76 | 81 | empty |
| 4 | 351 | 0.71 | 0.83 | 36 | PEG |
| 5 | 378 | 0.70 | 0.82 | 35 | EDO |
Interfaces
22 interfaces between chains.
- I–J · 2112 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 2075 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1475 Ų buried · 19 hydrogen bonds · protein-protein
- F–G · 1418 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1017 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 6VMX · Structure of HD14 TCR in complex with HLA-B7 presenting an EBV epitope · the same entry in another collection · chain J against J, 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
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 P01889
- Every structure of UniProt P61769
- Every structure of UniProt P12977
- Elsewhere: RCSB PDB 6VMX · PDBe 6VMX · UniProt P01889 · UniProt P61769 · UniProt P12977
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