MolNFT v1 · #84594 · protein
Acinetobacter baumannii ribd, form 2
3ZPG: “Acinetobacter baumannii ribd, form 2”. X-ray diffraction, 5 ligands (5GP, OXL, ZN), 4 pockets (best druggability 0.67). MolNFT v1 #84594 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3ZPG
- Type
- protein
- Length
- 354 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribd
- EC
- 3.5.4.26, 1.1.1.193
- UniProt
- D0CB74
- Ligands
- 5GP, OXL, ZN, SO4, CL
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribd (EC 3.5.4.26, 1.1.1.193) | protein | 354 | 34% helix, 24% strand | D0CB74 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 2 copies · chains A
- OXL · Oxalate ion · ligand · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- CAC · Cacodylate ion · additive · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.67 | 0.79 | 49 | SO4, 5GP, OXL, CL |
| 2 | 300 | 0.63 | 0.80 | 33 | SO4, CAC |
| 3 | 207 | 0.61 | 0.82 | 33 | ACT |
| 4 | 129 | 0.41 | 0.74 | 17 | empty |
Compared structures
- 3ZPG · Acinetobacter baumannii RibD, form 2 · 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 D0CB74
- Elsewhere: RCSB PDB 3ZPG · PDBe 3ZPG · UniProt D0CB74
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