MolNFT v1 · #188324 · protein
Crystal structure of ornithine carbamoyltransferase from klebsiella pneumoniae
7TMD: “Crystal structure of ornithine carbamoyltransferase from klebsiella pneumoniae”. X-ray diffraction, 2 ligands (BR, IOD), 15 pockets (best druggability 0.85). MolNFT v1 #188324 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7TMD
- Type
- protein
- Length
- 1,978 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ornithine carbamoyltransferase
- EC
- 2.1.3.3
- UniProt
- A0A0H3GHJ1
- Ligands
- BR, IOD
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 332 | 49% helix, 15% strand | A0A0H3GHJ1 |
| B | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 328 | 49% helix, 15% strand | A0A0H3GHJ1 |
| C | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 333 | 48% helix, 15% strand | A0A0H3GHJ1 |
| D | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 329 | 49% helix, 15% strand | A0A0H3GHJ1 |
| E | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 329 | 49% helix, 15% strand | A0A0H3GHJ1 |
| F | Ornithine carbamoyltransferase (EC 2.1.3.3) | protein | 327 | 49% helix, 15% strand | A0A0H3GHJ1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.85 | 0.88 | 107 | BR |
| 2 | 562 | 0.82 | 0.88 | 91 | BR |
| 3 | 309 | 0.76 | 0.87 | 44 | empty |
| 4 | 193 | 0.72 | 0.89 | 36 | empty |
| 5 | 179 | 0.68 | 0.87 | 29 | empty |
Interfaces
10 interfaces between chains.
- D–E · 1133 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1111 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1106 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1103 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 1043 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 7TMD · Crystal structure of Ornithine carbamoyltransferase from Klebsiella pneumoniae · 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 A0A0H3GHJ1
- Elsewhere: RCSB PDB 7TMD · PDBe 7TMD · UniProt A0A0H3GHJ1
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