MolNFT v1 · #7064 · protein
Crystal structure of human ornithine transcarbamylase complexed with carbamoyl phosphate
1FVO: “Crystal structure of human ornithine transcarbamylase complexed with carbamoyl phosphate”. X-ray diffraction, 1 ligand (CP), 5 pockets (best druggability 0.74). MolNFT v1 #7064 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1FVO
- Type
- protein
- Length
- 642 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ornithine transcarbamylase
- EC
- 2.1.3.3
- UniProt
- P00480
- Ligands
- CP
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ornithine transcarbamylase (EC 2.1.3.3) | protein | 321 | 42% helix, 15% strand | P00480 |
Ligands and binding sites
- CP · Phosphoric acid mono(formamide)ester · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.74 | 0.78 | 64 | CP |
| 2 | 358 | 0.59 | 0.77 | 30 | CP |
| 3 | 261 | 0.50 | 0.74 | 22 | empty |
| 4 | 70 | 0.47 | 0.82 | 18 | empty |
| 5 | 53 | 0.25 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 374 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1FVO · Crystal structure of human ornithine transcarbamylase complexed with carbamoyl phosphate · the same entry in another collection · chain B against B, TM-score 1.00
- P00480 · AlphaFold monomer V2.0 prediction for ornithine transcarbamylase, mitochondrial (P00480) · 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 P00480
- Elsewhere: RCSB PDB 1FVO · PDBe 1FVO · UniProt P00480
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