Research workbench
Crystal structure of predicted nucleotide-binding protein from vibrio cholerae
Analyse Crystal structure of predicted nucleotide-binding protein from vibrio cholerae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PMB
- Type
- protein
- Length
- 1,745 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q9KTK3
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 437 | 49% helix, 14% strand | Q9KTK3 |
| B | Uncharacterized protein | protein | 437 | 49% helix, 14% strand | Q9KTK3 |
| C | Uncharacterized protein | protein | 434 | 49% helix, 14% strand | Q9KTK3 |
| D | Uncharacterized protein | protein | 437 | 49% helix, 14% strand | Q9KTK3 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 12 copies · chains A, D, B, C
- GOL · Glycerol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.76 | 0.97 | 27 | PO4 |
| 2 | 77 | 0.74 | 0.98 | 25 | PO4 |
| 3 | 762 | 0.73 | 0.79 | 69 | empty |
| 4 | 783 | 0.73 | 0.78 | 70 | GOL |
| 5 | 190 | 0.71 | 0.89 | 41 | PO4 |
Interfaces
4 interfaces between chains.
- A–D · 1349 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1342 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1171 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1167 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 68 modified (engineered).
Compared structures
- 2PMB · Crystal structure of predicted nucleotide-binding protein from Vibrio cholerae · the same entry in another collection · chain C against C, TM-score 1.00
- 4NPA · Scrystal structure of protein with unknown function from vibrio cholerae at P22121… · an experimental structure of the same protein · chain C against A, TM-score 0.95
- 4NPA · Scrystal structure of protein with unknown function from Vibrio cholerae at P22121… · an experimental structure of the same protein · chain C against A, TM-score 0.95
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 Q9KTK3
- Elsewhere: RCSB PDB 2PMB · PDBe 2PMB · UniProt Q9KTK3 · AlphaFold DB Q9KTK3
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