MolNFT v1 · #183420 · protein
Crystal structure of mycobacterium tuberculosis argf in complex with (4-NITROPHENYL)BORONIC acid.
7NP0 · Ornithine carbamoyltransferase: “Crystal structure of mycobacterium tuberculosis argf in complex with (4-NITROPHENYL)BORONIC acid.”. X-ray diffraction, 2 ligands (UKH, PO4), 19 pockets (best druggability 0.88). MolNFT v1 #183420 on…
- PDB
- 7NP0
- Type
- protein
- Length
- 1,807 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ornithine carbamoyltransferase
- EC
- 2.1.3.3
- UniProt
- P9WIT9
- Ligands
- UKH, PO4
- Pockets
- 19 · best druggability 0.88
Structure
x-ray diffraction · 5 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 305 | 46% helix, 17% strand | P9WIT9 |
| B, D | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 298 | 45% helix, 17% strand | P9WIT9 |
| C | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 307 | 46% helix, 17% strand | P9WIT9 |
| E | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 299 | 46% helix, 17% strand | P9WIT9 |
| F | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 300 | 47% helix, 17% strand | P9WIT9 |
Ligands and binding sites
- UKH · p-nitrophenylboronic acid · ligand · 5 copies · chains B, C, A, D, F, E
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.88 | 0.90 | 95 | PO4 |
| 2 | 137 | 0.77 | 0.94 | 24 | empty |
| 3 | 392 | 0.74 | 0.85 | 49 | PO4, UKH |
| 4 | 438 | 0.74 | 0.84 | 49 | UKH, PO4 |
| 5 | 502 | 0.74 | 0.83 | 52 | UKH, PO4 |
Interfaces
9 interfaces between chains.
- A–B · 1055 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1050 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 1012 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 968 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 967 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 7NP0 · Crystal structure of Mycobacterium tuberculosis ArgF in complex with… · the same entry in another collection · chain F against F, TM-score 1.00
- P9WIT9 · AlphaFold monomer V2.0 prediction for ornithine carbamoyltransferase (P9WIT9) · a predicted model of the same protein · chain C 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 P9WIT9
- Elsewhere: RCSB PDB 7NP0 · PDBe 7NP0 · UniProt P9WIT9
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