MolNFT v1 · #82179 · protein
Crystal structure of the O-carbamoyltransferase tobz in complex with ampcpp and carbamoyl phosphate
3VES: “Crystal structure of the O-carbamoyltransferase tobz in complex with ampcpp and carbamoyl phosphate”. X-ray diffraction, 5 ligands (CP, APC, MN), 5 pockets (best druggability 0.84). MolNFT v1 #82179 on GenesisL1: 3D structure…
- PDB
- 3VES
- Type
- protein
- Length
- 567 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-carbamoyltransferase tobz
- EC
- 2.1.3.-
- UniProt
- Q70IY1
- Ligands
- CP, APC, MN, K, FE2
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-carbamoyltransferase tobz (EC 2.1.3.-) | protein | 567 | 37% helix, 21% strand | Q70IY1 |
Ligands and binding sites
- CP · Phosphoric acid mono(formamide)ester · ligand · chains A
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- K · Potassium ion · metal · chains A
- FE2 · Fe (II) ion · metal · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.84 | 0.86 | 78 | CP, APC, MN |
| 2 | 149 | 0.52 | 0.79 | 26 | empty |
| 3 | 79 | 0.32 | 0.74 | 16 | empty |
| 4 | 61 | 0.32 | 0.76 | 15 | empty |
| 5 | 65 | 0.30 | 0.75 | 15 | empty |
Compared structures
- 3VES · Crystal structure of the O-carbamoyltransferase TobZ in complex with AMPCPP and carbamoyl… · the same entry in another collection · chain A against A, TM-score 1.00
- Q70IY1 · AlphaFold monomer V2.0 prediction for nebramycin 5' synthase (Q70IY1) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q70IY1
- Elsewhere: RCSB PDB 3VES · PDBe 3VES · UniProt Q70IY1
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