MolNFT v1 · #190315 · protein
Crystal structure of HLA-A*2450 complexed with 8-mer model peptide
7WT5 · MHC class I antigen: “Crystal structure of HLA-A*2450 complexed with 8-mer model peptide”. X-ray diffraction, 1 ligand (ZN), 8 pockets (best druggability 0.71). MolNFT v1 #190315 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7WT5
- Type
- protein
- Length
- 733 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; 8-mer model peptide
- UniProt
- A0A109QAI7, P61769
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 20% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 277 | 28% helix, 40% strand | A0A109QAI7 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | 8-mer model peptide | protein | 8 | 0% helix, 0% strand | — |
| D | MHC class I antigen | protein | 243 | 29% helix, 33% strand | A0A109QAI7 |
| E | Beta-2-microglobulin | protein | 97 | 0% helix, 45% strand | P61769 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 47 copies · chains A, B, C, D, E, F
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.71 | 0.78 | 67 | EDO |
| 2 | 647 | 0.68 | 0.76 | 58 | EDO |
| 3 | 117 | 0.47 | 0.79 | 23 | empty |
| 4 | 111 | 0.45 | 0.78 | 22 | EDO |
| 5 | 160 | 0.44 | 0.75 | 32 | EDO |
Interfaces
4 interfaces between chains.
- A–B · 1299 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1216 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 868 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 842 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 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 A0A109QAI7
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 7WT5 · PDBe 7WT5 · UniProt A0A109QAI7 · UniProt P61769
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