MolNFT v1 · #138551 · protein
Crystal structure of HLA-B7 in complex with tpr, a CMV peptide
5WMP · HLA class I histocompatibility antigen, B-7 alpha chain: “Crystal structure of HLA-B7 in complex with tpr, a CMV peptide”. X-ray diffraction, 4 ligands (NA, ZN, IOD), 4 pockets (best druggability 0.69). MolNFT v1 #138551 on…
- PDB
- 5WMP
- Type
- protein
- Length
- 385 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-7 alpha chain; Beta-2-microglobulin; Tpr…
- UniProt
- P01889, P61769
- Ligands
- NA, ZN, IOD, CL
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-7 alpha chain | protein | 276 | 27% helix, 40% strand | P01889 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Tpr peptide from CMV | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A, B
- ZN · Zinc ion · metal · chains A, C
- IOD · Iodide ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 650 | 0.69 | 0.78 | 58 | IOD |
| 2 | 147 | 0.46 | 0.77 | 27 | empty |
| 3 | 53 | 0.35 | 0.79 | 18 | empty |
| 4 | 62 | 0.33 | 0.77 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1302 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 852 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5WMP · Crystal Structure of HLA-B7 in complex with TPR, a CMV peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P01889 · AlphaFold monomer V2.0 prediction for HLA class I histocompatibility antigen, B alpha… · a predicted model of the same protein · 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 0.98
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 P01889
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 5WMP · PDBe 5WMP · UniProt P01889 · UniProt P61769
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