Research workbench
Crystal structure of cowpox virus CPXV018 (omcp) bound to human NKG2D
Analyse Crystal structure of cowpox virus CPXV018 (omcp) bound to human NKG2D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PDC
- Type
- protein
- Length
- 791 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NKG2-D type II integral membrane protein; CPXV018 protein
- UniProt
- P26718, Q8QN43
- Pockets
- 18 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | NKG2-D type II integral membrane protein | protein | 123 | 11% helix, 41% strand | P26718 |
| B | NKG2-D type II integral membrane protein | protein | 122 | 11% helix, 45% strand | P26718 |
| E, F | CPXV018 protein | protein | 150 | 31% helix, 37% strand | Q8QN43 |
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.82 | 0.98 | 19 | empty |
| 2 | 174 | 0.74 | 0.91 | 27 | empty |
| 3 | 596 | 0.72 | 0.80 | 70 | empty |
| 4 | 354 | 0.64 | 0.79 | 60 | empty |
| 5 | 124 | 0.63 | 0.87 | 25 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1109 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1076 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 694 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 692 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 613 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 4PDC · Crystal structure of Cowpox virus CPXV018 (OMCP) bound to human NKG2D · the same entry in another collection · chain F against F, TM-score 1.00
- P26718 · AlphaFold monomer V2.0 prediction for NKG2-D type II integral membrane protein (P26718) · 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 P26718
- Every structure of UniProt Q8QN43
- Elsewhere: RCSB PDB 4PDC · PDBe 4PDC · UniProt P26718 · UniProt Q8QN43
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