Research workbench
Structure of VcINDY bound to Malate
Analyse Structure of VcINDY bound to Malate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OL0
- Type
- protein
- Length
- 1,712 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.502
- Source
- Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
- Molecule
- Transporter, NadC family
- UniProt
- Q9KNE0
- Ligands
- LMR, NA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · resolution 3.502 · 1 distinct chain · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, A, B | Transporter, NadC family | protein | 428 | 75% helix, 0% strand | Q9KNE0 |
Ligands and binding sites
- LMR · (2S)-2-hydroxybutanedioic acid · ligand · 4 copies · chains C, D, A, B
- NA · Sodium ion · metal · 6 copies · chains C, D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.82 | 0.99 | 17 | empty |
| 2 | 117 | 0.81 | 0.98 | 17 | empty |
| 3 | 783 | 0.70 | 0.77 | 77 | LMR |
| 4 | 61 | 0.68 | 0.95 | 13 | empty |
| 5 | 80 | 0.67 | 0.92 | 13 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2153 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2150 Ų buried · 22 hydrogen bonds · protein-protein
- D–A · 92 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6OL0 · Structure of vcindy bound to malate · the same entry in another collection · chain A against A, 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 Q9KNE0
- Elsewhere: RCSB PDB 6OL0 · PDBe 6OL0 · UniProt Q9KNE0
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