Research workbench
Crystal structure of H-2DB in complex with the W513S variant of jhmv epitope S510
Analyse Crystal structure of H-2DB in complex with the W513S variant of jhmv epitope… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZOL
- Type
- protein
- Length
- 728 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, D-B alpha chain; Beta-2-microglobulin; 9-meric…
- UniProt
- P01899, P01887, Q02385
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 258 | 28% helix, 38% strand | P01899 |
| C | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 256 | 28% helix, 38% strand | P01899 |
| D, B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P01887 |
| F, E | 9-meric peptide from spike glycoprotein | protein | 9 | 0% helix, 0% strand | Q02385 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.68 | 0.81 | 51 | empty |
| 2 | 336 | 0.66 | 0.81 | 35 | empty |
| 3 | 149 | 0.51 | 0.79 | 26 | empty |
| 4 | 137 | 0.47 | 0.78 | 33 | empty |
| 5 | 97 | 0.43 | 0.78 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1206 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1183 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 858 Ų buried · 24 hydrogen bonds · protein-protein
- C–F · 854 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 725 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 2ZOL · Crystal structure of H-2Db in complex with the W513S variant of JHMV epitope S510 · the same entry in another collection · chain E against E, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · 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 P01899
- Every structure of UniProt P01887
- Every structure of UniProt Q02385
- Elsewhere: RCSB PDB 2ZOL · PDBe 2ZOL · UniProt P01899 · UniProt P01887 · UniProt Q02385
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