Research workbench
Structural and functional study of succinyl-ornithine transaminase from E. COLI
Analyse Structural and functional study of succinyl-ornithine transaminase from E. COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ADD
- Type
- protein
- Length
- 1,600 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinylornithine transaminase
- EC
- 2.6.1.17, 2.6.1.81
- UniProt
- P77581
- Ligands
- PLP, SUO
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Succinylornithine transaminase (EC 2.6.1.17, 2.6.1.81) | protein | 400 | 42% helix, 19% strand | P77581 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- SUO · N~2~-(3-carboxypropanoyl)-L-ornithine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 429 | 0.83 | 0.91 | 59 | PLP, SUO |
| 2 | 407 | 0.83 | 0.91 | 62 | PLP, SUO |
| 3 | 535 | 0.79 | 0.86 | 67 | PLP, SUO |
| 4 | 549 | 0.79 | 0.85 | 57 | PLP, SUO |
| 5 | 241 | 0.76 | 0.89 | 40 | empty |
Interfaces
6 interfaces between chains.
- C–D · 4973 Ų buried · 62 hydrogen bonds · protein-protein
- A–B · 4936 Ų buried · 63 hydrogen bonds · protein-protein
- A–C · 278 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 246 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 205 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4ADD · Structural and functional study of succinyl-ornithine transaminase from E. coli · the same entry in another collection · chain D against D, TM-score 1.00
- P77581 · AlphaFold monomer V2.0 prediction for succinylornithine transaminase (P77581) · a predicted model of the same protein · chain D 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 P77581
- Elsewhere: RCSB PDB 4ADD · PDBe 4ADD · UniProt P77581
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