Research workbench
The crystal structure of the N-terminal domain of COMMD9
Analyse The crystal structure of the N-terminal domain of COMMD9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NKN
- Type
- protein
- Length
- 663 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Comm domain-containing protein 9
- UniProt
- Q9P000
- Pockets
- 10 · best druggability 0.64
Structure
x-ray diffraction · 5 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Comm domain-containing protein 9 | protein | 115 | 78% helix, 0% strand | Q9P000 |
| B | Comm domain-containing protein 9 | protein | 108 | 64% helix, 0% strand | Q9P000 |
| C, D | Comm domain-containing protein 9 | protein | 112 | 79% helix, 0% strand | Q9P000 |
| E | Comm domain-containing protein 9 | protein | 110 | 75% helix, 0% strand | Q9P000 |
| F | Comm domain-containing protein 9 | protein | 106 | 73% helix, 0% strand | Q9P000 |
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.64 | 0.81 | 25 | empty |
| 2 | 299 | 0.57 | 0.76 | 24 | empty |
| 3 | 248 | 0.49 | 0.74 | 27 | empty |
| 4 | 236 | 0.49 | 0.74 | 31 | empty |
| 5 | 187 | 0.47 | 0.75 | 32 | empty |
Interfaces
10 interfaces between chains.
- D–F · 1843 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1733 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 1710 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1691 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 1456 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 4NKN · The Crystal Structure of the N-terminal domain of COMMD9 · the same entry in another collection · chain F against F, TM-score 1.00
- Q9P000 · AlphaFold monomer V2.0 prediction for comm domain-containing protein 9 (Q9P000) · a predicted model of the same protein · chain D against A, TM-score 0.68
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 Q9P000
- Elsewhere: RCSB PDB 4NKN · PDBe 4NKN · UniProt Q9P000
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