Research workbench
Crystal structure of E. COLI ornithine transcarbamoylase complexed with ndelta-L-ornithine-diaminophosphinyl-N- sulphonic acid (psorn)
Analyse Crystal structure of E. COLI ornithine transcarbamoylase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DUV
- Type
- protein
- Length
- 999 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ornithine transcarbamoylase
- EC
- 2.1.3.3
- UniProt
- P04391
- Ligands
- PSQ
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, H, I | Ornithine transcarbamoylase (EC 2.1.3.3) | protein | 333 | 46% helix, 15% strand | P04391 |
Ligands and binding sites
- PSQ · Ndelta-(N'-sulphodiaminophosphinyl)-L-ornithine · ligand · 3 copies · chains G, I, H
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.76 | 0.92 | 38 | empty |
| 2 | 81 | 0.71 | 0.96 | 23 | PSQ |
| 3 | 90 | 0.69 | 0.93 | 27 | PSQ |
| 4 | 106 | 0.68 | 0.91 | 30 | PSQ |
| 5 | 104 | 0.34 | 0.74 | 22 | empty |
Interfaces
3 interfaces between chains.
- G–H · 1368 Ų buried · 22 hydrogen bonds · protein-protein
- H–I · 1366 Ų buried · 24 hydrogen bonds · protein-protein
- G–I · 1324 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 1DUV · Crystal structure of E. COLI ornithine transcarbamoylase complexed with… · the same entry in another collection · chain G against G, TM-score 1.00
- P04391 · AlphaFold monomer V2.0 prediction for ornithine carbamoyltransferase subunit I (P04391) · a predicted model of the same protein · chain G 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 P04391
- Elsewhere: RCSB PDB 1DUV · PDBe 1DUV · UniProt P04391
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