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Crystal structure analysis of ornithine cyclodeaminase complexed with NAD and ornithine to 1.6 ångströms
Analyse Crystal structure analysis of ornithine cyclodeaminase complexed with NAD and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1X7D
- Type
- protein
- Length
- 679 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ornithine cyclodeaminase
- EC
- 4.3.1.12
- UniProt
- Q88H32
- Ligands
- NAD, ORN, NA
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ornithine cyclodeaminase (EC 4.3.1.12) | protein | 340 | 37% helix, 25% strand | Q88H32 |
| B | Ornithine cyclodeaminase (EC 4.3.1.12) | protein | 339 | 39% helix, 25% strand | Q88H32 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- ORN · L-ornithine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 6 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.78 | 0.89 | 54 | ORN, NAD |
| 2 | 285 | 0.77 | 0.89 | 48 | NAD, ORN |
Interfaces
1 interface between chains.
- A–B · 3810 Ų buried · 50 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 1X7D · Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed with NAD and ornithine… · the same entry in another collection · chain A against A, TM-score 1.00
- Q88H32 · AlphaFold monomer V2.0 prediction for ornithine cyclodeaminase (Q88H32) · 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 Q88H32
- Elsewhere: RCSB PDB 1X7D · PDBe 1X7D · UniProt Q88H32
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