MolNFT v1 · #47686 · protein
Crystal structures of high affinity human T-cell receptors bound to pmhc reveal native diagonal binding geometry
2P5W · HLA class I histocompatibility antigen, a-2 alpha chain: “Crystal structures of high affinity human T-cell receptors bound to pmhc reveal native diagonal binding…”. X-ray diffraction, 3 ligands (CA, MG, SO4), 11 pockets (best…
- PDB
- 2P5W
- Type
- protein
- Length
- 819 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin…
- UniProt
- P01892, P61769, P78358, Q6PIZ8, Q2YDB4
- Ligands
- CA, MG, SO4
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 276 | 27% helix, 40% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | CANCER/TESTIS antigen 1B | protein | 9 | 0% helix, 0% strand | P78358 |
| D | T-cell receptor, alpha chain | protein | 192 | 3% helix, 51% strand | Q6PIZ8 |
| E | Hypothetical protein | protein | 242 | 7% helix, 50% strand | Q2YDB4 |
Ligands and binding sites
- CA · Calcium ion · metal · chains B
- MG · Magnesium ion · metal · chains B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, D, E
- GOL · Glycerol · additive · 11 copies · chains A, B, D, E
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.73 | 0.76 | 80 | empty |
| 2 | 609 | 0.68 | 0.77 | 53 | GOL |
| 3 | 168 | 0.53 | 0.79 | 37 | GOL |
| 4 | 198 | 0.49 | 0.76 | 39 | empty |
| 5 | 62 | 0.43 | 0.82 | 18 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2068 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1375 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 822 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 488 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 408 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2P5W · Crystal structures of high affinity human T-cell receptors bound to pMHC reveal native… · the same entry in another collection · chain B against B, 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
- P78358 · AlphaFold monomer V2.0 prediction for CANCER/TESTIS antigen 1 (P78358) · a predicted model of the same protein · chain C against A, TM-score 0.29
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 P01892
- Every structure of UniProt P61769
- Every structure of UniProt P78358
- Every structure of UniProt Q6PIZ8
- Every structure of UniProt Q2YDB4
- Elsewhere: RCSB PDB 2P5W · PDBe 2P5W · UniProt P01892 · UniProt P61769 · UniProt P78358 · UniProt Q6PIZ8 · UniProt Q2YDB4
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