MolNFT v1 · #154785 · protein
Crystal structure of suca from vibrio vulnificus
6KM9 · Oxoglutarate dehydrogenase (succinyl-transferring), E1…: “Crystal structure of suca from vibrio vulnificus”. X-ray diffraction, 3 ligands (TPP, MG, CA), 20 pockets (best druggability 0.81). MolNFT v1 #154785 on GenesisL1: 3D…
- PDB
- 6KM9
- Type
- protein
- Length
- 1,689 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxoglutarate dehydrogenase (succinyl-transferring), E1 component
- EC
- 1.2.4.2
- UniProt
- A0A3Q0L1E1
- Ligands
- TPP, MG, CA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxoglutarate dehydrogenase (succinyl-transferring), E1 component (EC 1.2.4.2) | protein | 844 | 43% helix, 15% strand | A0A3Q0L1E1 |
| B | Oxoglutarate dehydrogenase (succinyl-transferring), E1 component (EC 1.2.4.2) | protein | 845 | 43% helix, 15% strand | A0A3Q0L1E1 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · chains A, B
- P6G · Hexaethylene glycol · additive · 2 copies · chains 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.81 | 0.88 | 66 | TPP |
| 2 | 908 | 0.81 | 0.83 | 111 | MG, TPP, CA |
| 3 | 823 | 0.77 | 0.81 | 68 | empty |
| 4 | 738 | 0.75 | 0.80 | 79 | empty |
| 5 | 496 | 0.75 | 0.83 | 58 | empty |
Interfaces
1 interface between chains.
- A–B · 5076 Ų buried · 90 hydrogen bonds · protein-protein
Compared structures
- 6KM9 · Crystal structure of SucA from Vibrio vulnificus · 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 A0A3Q0L1E1
- Elsewhere: RCSB PDB 6KM9 · PDBe 6KM9 · UniProt A0A3Q0L1E1
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