MolNFT v1 · #154786 · protein
Crystal structure of suca with glycolaldehyde-1-13C from vibrio vulnificus
6KMA · Oxoglutarate dehydrogenase (succinyl-transferring), E1…: “Crystal structure of suca with glycolaldehyde-1-13C from vibrio vulnificus”. X-ray diffraction, 4 ligands (DW3, TPP, MG), 20 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 6KMA
- Type
- protein
- Length
- 3,351 residues
- Chains
- 4
- 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
- DW3, TPP, MG, CA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxoglutarate dehydrogenase (succinyl-transferring), E1 component (EC 1.2.4.2) | protein | 839 | 44% helix, 15% strand | A0A3Q0L1E1 |
| B | Oxoglutarate dehydrogenase (succinyl-transferring), E1 component (EC 1.2.4.2) | protein | 837 | 44% helix, 15% strand | A0A3Q0L1E1 |
| C | Oxoglutarate dehydrogenase (succinyl-transferring), E1 component (EC 1.2.4.2) | protein | 839 | 44% helix, 15% strand | A0A3Q0L1E1 |
| D | Oxoglutarate dehydrogenase (succinyl-transferring), E1 component (EC 1.2.4.2) | protein | 836 | 44% helix, 15% strand | A0A3Q0L1E1 |
Ligands and binding sites
- DW3 · 2-oxidanylethanal · ligand · 8 copies · chains A, B, C, D
- TPP · Thiamine diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, B, C, D
- P6G · Hexaethylene glycol · additive · 4 copies · chains A, B, C, 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1107 | 0.81 | 0.83 | 124 | empty |
| 2 | 786 | 0.80 | 0.83 | 102 | TPP, DW3 |
| 3 | 832 | 0.80 | 0.83 | 111 | DW3, MG, TPP |
| 4 | 563 | 0.80 | 0.86 | 84 | TPP, DW3 |
| 5 | 1143 | 0.80 | 0.81 | 101 | empty |
Interfaces
5 interfaces between chains.
- A–B · 5128 Ų buried · 87 hydrogen bonds · protein-protein
- C–D · 5012 Ų buried · 88 hydrogen bonds · protein-protein
- B–C · 235 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 170 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 79 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6KMA · Crystal structure of SucA with glycolaldehyde-1-13C 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 6KMA · PDBe 6KMA · UniProt A0A3Q0L1E1
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