MolNFT v1 · #50356 · protein
Crystal structure of HLA-B*5701, presenting the self peptide, lsspvtksf
2RFX · HLA class I histocompatibility antigen, B-57 alpha chain: “Crystal structure of HLA-B*5701, presenting the self peptide, lsspvtksf”. X-ray diffraction, 3 pockets (best druggability 0.70). MolNFT v1 #50356 on GenesisL1: 3D structure…
- PDB
- 2RFX
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-57 alpha chain; Beta-2-microglobulin; Lsspvtksf
- UniProt
- P18465, P61769
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-57 alpha chain | protein | 275 | 25% helix, 39% strand | P18465 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Lsspvtksf | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 583 | 0.70 | 0.79 | 55 | empty |
| 2 | 116 | 0.46 | 0.79 | 20 | empty |
| 3 | 59 | 0.43 | 0.82 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1389 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 819 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2RFX · Crystal Structure of HLA-B*5701, presenting the self peptide, LSSPVTKSF · the same entry in another collection · chain A against A, 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 0.99
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 P18465
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 2RFX · PDBe 2RFX · UniProt P18465 · UniProt P61769
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