MolNFT v1 · #166849 · protein
HLA-B*57:03 presenting the peptide aslnlpavsw
6V2P · HLA-B alpha chain (B*5703GB): “HLA-B*57:03 presenting the peptide aslnlpavsw”. X-ray diffraction, 5 pockets (best druggability 0.70). MolNFT v1 #166849 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6V2P
- Type
- protein
- Length
- 386 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA-B alpha chain (B*5703GB); Beta-2-microglobulin; Peptide…
- UniProt
- I3ZN84, P61769
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA-B alpha chain (B*5703GB) | protein | 276 | 27% helix, 39% strand | I3ZN84 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Peptide ala-ser-leu-asn-leu-pro-ala-val-ser-TRP | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 651 | 0.70 | 0.78 | 53 | empty |
| 2 | 58 | 0.61 | 0.92 | 20 | empty |
| 3 | 175 | 0.50 | 0.77 | 37 | empty |
| 4 | 97 | 0.45 | 0.80 | 23 | ACT |
| 5 | 55 | 0.34 | 0.78 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1352 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 787 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 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 I3ZN84
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6V2P · PDBe 6V2P · UniProt I3ZN84 · UniProt P61769
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