MolNFT v1 · #179140 · protein
Crystal structure of B17.R2 TCR in complex with H2D-B-NP366
7JWI · H-2 class I histocompatibility antigen, D-B alpha chain: “Crystal structure of B17.R2 TCR in complex with H2D-B-NP366”. X-ray diffraction, 9 pockets (best druggability 0.71). MolNFT v1 #179140 on GenesisL1: 3D structure, binding…
- PDB
- 7JWI
- Type
- protein
- Length
- 828 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, D-B alpha chain; Beta-2-microglobulin…
- UniProt
- P01899, P61769, Q9Q0U8
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 277 | 26% helix, 39% strand | P01899 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Nucleoprotein | protein | 9 | 0% helix, 0% strand | Q9Q0U8 |
| D | B17.R2 TCR alpha chain | protein | 203 | 3% helix, 45% strand | — |
| E | B17.R2 TCR beta chain | protein | 240 | 6% helix, 48% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.71 | 0.75 | 82 | empty |
| 2 | 640 | 0.68 | 0.77 | 56 | empty |
| 3 | 74 | 0.62 | 0.91 | 24 | empty |
| 4 | 291 | 0.52 | 0.74 | 33 | empty |
| 5 | 59 | 0.39 | 0.80 | 18 | empty |
Interfaces
6 interfaces between chains.
- D–E · 2223 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1362 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 896 Ų buried · 28 hydrogen bonds · protein-protein
- A–E · 645 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 307 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
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 P01899
- Every structure of UniProt P61769
- Every structure of UniProt Q9Q0U8
- Elsewhere: RCSB PDB 7JWI · PDBe 7JWI · UniProt P01899 · UniProt P61769 · UniProt Q9Q0U8
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