Research workbench
Structure of vcindy bound to fumarate
Analyse Structure of vcindy bound to fumarate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OKZ
- Type
- protein
- Length
- 1,752 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transporter, nadc family
- UniProt
- Q9KNE0
- Ligands
- FUM, NA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | Transporter, nadc family | protein | 432 | 76% helix, 0% strand | Q9KNE0 |
| D, B | Transporter, nadc family | protein | 444 | 74% helix, 0% strand | Q9KNE0 |
Ligands and binding sites
- FUM · Fumaric acid · ligand · 2 copies · chains C, B
- NA · Sodium ion · metal · 7 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.80 | 0.99 | 16 | empty |
| 2 | 90 | 0.79 | 0.99 | 15 | empty |
| 3 | 62 | 0.68 | 0.95 | 15 | empty |
| 4 | 55 | 0.68 | 0.95 | 12 | empty |
| 5 | 556 | 0.67 | 0.77 | 47 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2122 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2114 Ų buried · 20 hydrogen bonds · protein-protein
- D–B · 293 Ų buried · 3 hydrogen bonds · protein-protein
- C–B · 70 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6OKZ · Structure of VcINDY bound to Fumarate · the same entry in another collection · chain C against C, 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 6OKZ · PDBe 6OKZ · UniProt Q9KNE0
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