MolNFT v1 · #135780 · protein
The crystal structure of a self-peptide complexed to abacavir and HLA- B*57:01
5U98 · HLA class I histocompatibility antigen, B-57 alpha chain: “The crystal structure of a self-peptide complexed to abacavir and HLA- B*57:01”. X-ray diffraction, 1 ligand (1KX), 10 pockets (best druggability 0.82). MolNFT v1 #135780 on…
- PDB
- 5U98
- Type
- protein
- Length
- 762 residues
- Chains
- 6
- 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…
- UniProt
- P18465, P61769
- Ligands
- 1KX
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class I histocompatibility antigen, B-57 alpha chain | protein | 273 | 28% helix, 40% strand | P18465 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C, F | Val-thr-thr-asp-ile-gln-val-lys-val | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- 1KX · {(1S,4R)-4-[2-amino-6-(cyclopropylamino)-9H-purin-9-yl]cyclopent-2-en-1-yl}methanol · ligand · 2 copies · chains A, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.82 | 0.83 | 112 | empty |
| 2 | 134 | 0.81 | 0.98 | 27 | 1KX |
| 3 | 138 | 0.81 | 0.97 | 28 | 1KX |
| 4 | 539 | 0.70 | 0.79 | 47 | empty |
| 5 | 443 | 0.68 | 0.79 | 39 | empty |
Interfaces
7 interfaces between chains.
- D–E · 1403 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1386 Ų buried · 26 hydrogen bonds · protein-protein
- D–F · 775 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 767 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 281 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5U98 · The crystal structure of a self-peptide complexed to Abacavir and HLA-B*57:01 · the same entry in another collection · chain F against F, 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
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 5U98 · PDBe 5U98 · UniProt P18465 · UniProt P61769
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