MolNFT v1 · #159303 · protein
Structure of vcindy in complex with succinate
6OL1 · Transporter, nadc family: “Structure of vcindy in complex with succinate”. X-ray diffraction, 1 ligand (NA), 20 pockets (best druggability 0.82). MolNFT v1 #159303 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6OL1
- Type
- protein
- Length
- 1,780 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transporter, nadc family
- UniProt
- Q9KNE0
- Ligands
- NA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, A, B | Transporter, nadc family | protein | 445 | 73% helix, 0% strand | Q9KNE0 |
Ligands and binding sites
- NA · Sodium ion · metal · 8 copies · chains C, D, A, B
- SIN · Succinic acid · additive · 4 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 | 125 | 0.82 | 0.99 | 16 | empty |
| 2 | 119 | 0.81 | 0.98 | 16 | empty |
| 3 | 960 | 0.74 | 0.77 | 89 | SIN |
| 4 | 58 | 0.67 | 0.95 | 13 | empty |
| 5 | 326 | 0.66 | 0.80 | 42 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2104 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 2084 Ų buried · 17 hydrogen bonds · protein-protein
- D–B · 270 Ų buried · 4 hydrogen bonds · protein-protein
- C–B · 97 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6OL1 · Structure of VcINDY in complex with Succinate · 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 6OL1 · PDBe 6OL1 · UniProt Q9KNE0
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