MolNFT v1 · #156425 · protein
Dimeric isocitrate dehydrogenase from xanthomonas campestris pv. campestris 8004
6M3S: “Dimeric isocitrate dehydrogenase from xanthomonas campestris pv. campestris 8004”. X-ray diffraction, 2 ligands (NAD, ICA), 10 pockets (best druggability 0.54). MolNFT v1 #156425 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6M3S
- Type
- protein
- Length
- 671 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase
- EC
- 1.1.1.41
- UniProt
- A0A2S4JWD6
- Ligands
- NAD, ICA
- Pockets
- 10 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase (EC 1.1.1.41) | protein | 333 | 43% helix, 18% strand | A0A2S4JWD6 |
| B | Isocitrate dehydrogenase (EC 1.1.1.41) | protein | 338 | 43% helix, 18% strand | A0A2S4JWD6 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- ICA · Isocitrate calcium complex · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.54 | 0.77 | 24 | empty |
| 2 | 235 | 0.53 | 0.76 | 26 | empty |
| 3 | 62 | 0.46 | 0.83 | 13 | GOL |
| 4 | 196 | 0.46 | 0.75 | 33 | ICA |
| 5 | 60 | 0.45 | 0.83 | 12 | GOL |
Interfaces
1 interface between chains.
- A–B · 477 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6M3S · Dimeric isocitrate dehydrogenase from Xanthomonas campestris pv. campestris 8004 · 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 A0A2S4JWD6
- Elsewhere: RCSB PDB 6M3S · PDBe 6M3S · UniProt A0A2S4JWD6
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