Research workbench
Crystal structure of the binary complex between HLA-A2 and hcmv nlv- M5S peptide variant
Analyse Crystal structure of the binary complex between HLA-A2 and hcmv nlv- M5S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GSQ
- 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, a-2 alpha chain; Beta-2-microglobulin; Hcmv PP65…
- UniProt
- P01892, P61769
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 274 | 26% helix, 41% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| P | Hcmv PP65 fragment 495-503, variant M5S (nlvpsvatv) | protein | 9 | 0% helix, 0% strand | — |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 524 | 0.67 | 0.78 | 46 | empty |
| 2 | 125 | 0.53 | 0.81 | 23 | empty |
| 3 | 161 | 0.47 | 0.77 | 32 | empty |
| 4 | 73 | 0.39 | 0.79 | 15 | empty |
| 5 | 76 | 0.31 | 0.74 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1384 Ų buried · 20 hydrogen bonds · protein-protein
- A–P · 785 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3GSQ · Crystal structure of the binary complex between HLA-A2 and HCMV NLV-M5S peptide variant · 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 0.97
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 P01892
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 3GSQ · PDBe 3GSQ · UniProt P01892 · UniProt P61769
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