MolNFT v1 · #71999 · protein
Crystal structure of the TK3-GLN55ALA TCR in complex with HLA- B*3501/HPVG
3MV9 · HLA class I histocompatibility antigen, B-35 alpha chain: “Crystal structure of the TK3-GLN55ALA TCR in complex with HLA- B*3501/HPVG”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.71). MolNFT v1 #71999 on…
- PDB
- 3MV9
- Type
- protein
- Length
- 828 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-35 alpha chain; Beta-2-microglobulin; Hpvg…
- UniProt
- P30685, P61769, P03211
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-35 alpha chain | protein | 276 | 24% helix, 32% strand | P30685 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 37% strand | P61769 |
| C | Hpvg peptide from epstein-barr nuclear antigen 1 | protein | 11 | 0% helix, 0% strand | P03211 |
| D | Alpha chain of the TK3 TCR | protein | 200 | 3% helix, 38% strand | — |
| E | Beta chain of the TK3 TCR | protein | 241 | 7% helix, 48% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.71 | 0.75 | 77 | empty |
| 2 | 553 | 0.67 | 0.78 | 57 | empty |
| 3 | 82 | 0.49 | 0.83 | 22 | empty |
| 4 | 189 | 0.46 | 0.75 | 31 | empty |
| 5 | 121 | 0.41 | 0.76 | 23 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2199 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1345 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 903 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 390 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 301 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3MV9 · Crystal Structure of the TK3-Gln55Ala TCR in complex with HLA-B*3501/HPVG · the same entry in another collection · chain D against D, 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 0.96
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 P30685
- Every structure of UniProt P61769
- Every structure of UniProt P03211
- Elsewhere: RCSB PDB 3MV9 · PDBe 3MV9 · UniProt P30685 · UniProt P61769 · UniProt P03211
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