MolNFT v1 · #52514 · protein
Crystal structure of the hexameric catabolic ornithine transcarbamylase from lactobacillus hilgardii
2W37 · Ornithine carbamoyltransferase, catabolic: “Crystal structure of the hexameric catabolic ornithine transcarbamylase from lactobacillus hilgardii”. X-ray diffraction, 1 ligand (NI), 7 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 2W37
- Type
- protein
- Length
- 1,023 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ornithine carbamoyltransferase, catabolic
- EC
- 2.1.3.3
- UniProt
- Q8G998
- Ligands
- NI
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ornithine carbamoyltransferase, catabolic (EC 2.1.3.3) | protein | 341 | 47% helix, 14% strand | Q8G998 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 673 | 0.77 | 0.82 | 58 | empty |
| 2 | 629 | 0.76 | 0.82 | 58 | empty |
| 3 | 621 | 0.73 | 0.80 | 58 | empty |
| 4 | 170 | 0.72 | 0.90 | 22 | empty |
| 5 | 543 | 0.68 | 0.78 | 46 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1178 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1152 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1101 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2W37 · CRYSTAL STRUCTURE OF THE HEXAMERIC CATABOLIC ORNITHINE TRANSCARBAMYLASE FROM… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8G998 · AlphaFold monomer V2.0 prediction for ornithine carbamoyltransferase, catabolic (Q8G998) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q8G998
- Elsewhere: RCSB PDB 2W37 · PDBe 2W37 · UniProt Q8G998
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