Research workbench
Crystal structure of mycobacterium tuberculosis argf in complex with carbamoyl phosphate.
Analyse Crystal structure of mycobacterium tuberculosis argf in complex with carbamoyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NNV
- Type
- protein
- Length
- 1,814 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
- CP, PO4
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 308 | 43% helix, 15% strand | P9WIT9 |
| B | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 298 | 45% helix, 16% strand | P9WIT9 |
| C | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 307 | 44% helix, 16% strand | P9WIT9 |
| D | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 300 | 44% helix, 16% strand | P9WIT9 |
| E | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 299 | 43% helix, 17% strand | P9WIT9 |
| F | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 302 | 45% helix, 17% strand | P9WIT9 |
Ligands and binding sites
- CP · Phosphoric acid mono(formamide)ester · ligand · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 9 copies · chains A, B, C, D, E
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.83 | 0.84 | 62 | empty |
| 2 | 91 | 0.73 | 0.96 | 19 | empty |
| 3 | 439 | 0.72 | 0.82 | 50 | CP |
| 4 | 116 | 0.72 | 0.94 | 22 | empty |
| 5 | 315 | 0.67 | 0.82 | 41 | CP |
Interfaces
12 interfaces between chains.
- D–F · 1163 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1159 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1138 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1126 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1124 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 7NNV · Crystal structure of Mycobacterium tuberculosis ArgF in complex with carbamoyl phosphate. · 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 B 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 7NNV · PDBe 7NNV · UniProt P9WIT9
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