MolNFT v1 · #52799 · protein
TCR COMPLEX
2WBJ · HLA class II histocompatibility antigen, dr alpha chain: “TCR COMPLEX”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.73). MolNFT v1 #52799 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2WBJ
- Type
- protein
- Length
- 1,635 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, dr alpha chain; HLA class II histocompatibility…
- UniProt
- P01903, P01911
- Ligands
- NAG, MAN, BMA, SO4
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 8 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 178 | 15% helix, 47% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-15 beta chain | protein | 179 | 20% helix, 44% strand | P01911 |
| C | Ob TCR | protein | 193 | 2% helix, 46% strand | — |
| D | Ob TCR | protein | 270 | 5% helix, 45% strand | — |
| E | HLA class II histocompatibility antigen, dr alpha chain | protein | 177 | 15% helix, 47% strand | P01903 |
| F | HLA class II histocompatibility antigen, DRB1-15 beta chain | protein | 188 | 18% helix, 43% strand | P01911 |
| G | Ob TCR | protein | 190 | 2% helix, 42% strand | — |
| H | Ob TCR | protein | 260 | 5% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains E, F, A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains F
- BMA · beta-D-mannopyranose · sugar · chains F
- SO4 · Sulfate ion · ion · 3 copies · chains B, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.73 | 0.77 | 76 | empty |
| 2 | 1161 | 0.72 | 0.76 | 88 | empty |
| 3 | 56 | 0.65 | 0.94 | 19 | empty |
| 4 | 522 | 0.62 | 0.75 | 44 | empty |
| 5 | 390 | 0.59 | 0.76 | 48 | empty |
Interfaces
14 interfaces between chains.
- A–B · 2600 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 2523 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2465 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 2277 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 904 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 2WBJ · TCR complex · the same entry in another collection · chain H against H, TM-score 1.00
- P01911 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, DRB1 beta… · a predicted model of the same protein · chain B against A, TM-score 0.97
- P01903 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dr alpha… · a predicted model of the same protein · chain E 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 P01903
- Every structure of UniProt P01911
- Elsewhere: RCSB PDB 2WBJ · PDBe 2WBJ · UniProt P01903 · UniProt P01911
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