Research workbench
Crystal structure of HLA-B*37:01 in complex with NP338 influenza peptide
Analyse Crystal structure of HLA-B*37:01 in complex with NP338 influenza peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MT6
- Type
- protein
- Length
- 384 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-37 alpha chain; NP388 peptide…
- UniProt
- P18463, P61769
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-37 alpha chain | protein | 276 | 28% helix, 39% strand | P18463 |
| B | NP388 peptide | protein | 9 | 0% helix, 0% strand | — |
| C | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
Ligands and binding sites
- ACT · Acetate ion · additive · 2 copies · chains A, C
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 | 615 | 0.69 | 0.77 | 53 | empty |
| 2 | 124 | 0.44 | 0.77 | 26 | empty |
| 3 | 72 | 0.39 | 0.78 | 14 | empty |
| 4 | 61 | 0.37 | 0.79 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1329 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 983 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6MT6 · Crystal Structure of HLA-B*37:01 in complex with NP338 influenza peptide · 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 C 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 P18463
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6MT6 · PDBe 6MT6 · UniProt P18463 · UniProt P61769
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