Research workbench
Scrystal structure of protein with unknown function from vibrio cholerae at P22121 spacegroup
Analyse Scrystal structure of protein with unknown function from vibrio cholerae at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NPA
- Type
- protein
- Length
- 1,669 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein
- UniProt
- Q9KTK3
- Ligands
- PO4, SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein | protein | 418 | 51% helix, 12% strand | Q9KTK3 |
| B | Putative uncharacterized protein | protein | 420 | 51% helix, 13% strand | Q9KTK3 |
| C | Putative uncharacterized protein | protein | 418 | 50% helix, 13% strand | Q9KTK3 |
| D | Putative uncharacterized protein | protein | 413 | 51% helix, 13% strand | Q9KTK3 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains B, C, D
- SO4 · Sulfate ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.77 | 0.80 | 98 | empty |
| 2 | 107 | 0.71 | 0.93 | 25 | PO4 |
| 3 | 814 | 0.71 | 0.77 | 82 | empty |
| 4 | 282 | 0.71 | 0.85 | 55 | PEG |
| 5 | 177 | 0.70 | 0.88 | 45 | PO4 |
Interfaces
4 interfaces between chains.
- B–C · 1275 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1220 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1181 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1104 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 4NPA · Scrystal structure of protein with unknown function from Vibrio cholerae at P22121… · the same entry in another collection · chain B against B, TM-score 1.00
- 3GH1 · Crystal structure of predicted nucleotide-binding protein from Vibrio cholerae · a predicted model of the same protein · chain D against D, TM-score 1.00
- 3GH1 · Crystal structure of predicted nucleotide-binding protein from vibrio cholerae · a predicted model of the same protein · chain D against D, TM-score 1.00
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 4NPA · PDBe 4NPA · UniProt Q9KTK3
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