MolNFT v1 · #122657 · protein
Crystal structure of B4.2.3 T-cell receptor and H2-dd P18-I10 complex
5IVX · H-2 class I histocompatibility antigen, D-D alpha chain: “Crystal structure of B4.2.3 T-cell receptor and H2-dd P18-I10 complex”. X-ray diffraction, 12 pockets (best druggability 0.71). MolNFT v1 #122657 on GenesisL1: 3D structure…
- PDB
- 5IVX
- Type
- protein
- Length
- 811 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, D-D alpha chain; Beta-2-microglobulin; T-cell…
- UniProt
- P01900, P01887
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, D-D alpha chain | protein | 274 | 27% helix, 38% strand | P01900 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| E | T-cell receptor alpha chain | protein | 194 | 2% helix, 44% strand | — |
| F | T-cell receptor beta chain | protein | 234 | 7% helix, 52% strand | — |
| P | P18-I10 | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, E, F, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 842 | 0.71 | 0.77 | 63 | empty |
| 2 | 563 | 0.64 | 0.76 | 52 | empty |
| 3 | 239 | 0.58 | 0.79 | 40 | empty |
| 4 | 98 | 0.48 | 0.81 | 24 | empty |
| 5 | 73 | 0.43 | 0.81 | 18 | EDO |
Interfaces
7 interfaces between chains.
- E–F · 2036 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1334 Ų buried · 18 hydrogen bonds · protein-protein
- A–P · 911 Ų buried · 23 hydrogen bonds · protein-protein
- A–F · 496 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 435 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 5IVX · Crystal Structure of B4.2.3 T-Cell Receptor and H2-Dd P18-I10 Complex · the same entry in another collection · chain B against B, TM-score 1.00
- P01900 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, D-D alpha… · a predicted model of the same protein · chain A against A, TM-score 0.97
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · 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 P01900
- Every structure of UniProt P01887
- Elsewhere: RCSB PDB 5IVX · PDBe 5IVX · UniProt P01900 · UniProt P01887
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