MolNFT v1 · #141248 · protein
A novel dimeric isocitrate dehydrogenase from acinetobacter baumannii
5Z16: “A novel dimeric isocitrate dehydrogenase from acinetobacter baumannii”. X-ray diffraction, 2 ligands (MG, PO4), 16 pockets (best druggability 0.76). MolNFT v1 #141248 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5Z16
- Type
- protein
- Length
- 1,474 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase
- EC
- 1.1.1.42
- UniProt
- V5VCI0
- Ligands
- MG, PO4
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase (EC 1.1.1.42) | protein | 735 | 40% helix, 17% strand | V5VCI0 |
| B | Isocitrate dehydrogenase (EC 1.1.1.42) | protein | 739 | 48% helix, 16% strand | V5VCI0 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.76 | 0.79 | 86 | empty |
| 2 | 65 | 0.75 | 0.99 | 24 | empty |
| 3 | 71 | 0.75 | 0.98 | 25 | empty |
| 4 | 724 | 0.74 | 0.80 | 102 | MG |
| 5 | 268 | 0.66 | 0.82 | 44 | empty |
Interfaces
1 interface between chains.
- A–B · 1316 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5Z16 · A novel dimeric isocitrate dehydrogenase from Acinetobacter baumannii · 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 V5VCI0
- Elsewhere: RCSB PDB 5Z16 · PDBe 5Z16 · UniProt V5VCI0
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