Research workbench
A dimer interface mutant of ornithine decarboxylase reveals structure of gem diamine intermediate
Analyse A dimer interface mutant of ornithine decarboxylase reveals structure of gem… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SZR
- Type
- protein
- Length
- 1,414 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ornithine decarboxylase
- EC
- 4.1.1.17
- UniProt
- P07805
- Ligands
- PXP, PLG, ORX
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Ornithine decarboxylase (EC 4.1.1.17) | protein | 347 | 34% helix, 24% strand | P07805 |
| D | Ornithine decarboxylase (EC 4.1.1.17) | protein | 368 | 34% helix, 24% strand | P07805 |
| A | Ornithine decarboxylase (EC 4.1.1.17) | protein | 345 | 36% helix, 25% strand | P07805 |
| B | Ornithine decarboxylase (EC 4.1.1.17) | protein | 354 | 37% helix, 24% strand | P07805 |
Ligands and binding sites
- PXP · Pyridoxine-5'-phosphate · ligand · 2 copies · chains C, D
- PLG · N-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane] · ligand · chains A, B
- ORX · N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-D-ornithine · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.70 | 0.81 | 60 | ORX |
| 2 | 441 | 0.69 | 0.80 | 60 | PLG |
| 3 | 739 | 0.65 | 0.74 | 90 | empty |
| 4 | 263 | 0.64 | 0.82 | 43 | PXP |
| 5 | 232 | 0.63 | 0.82 | 46 | PXP |
Interfaces
4 interfaces between chains.
- C–D · 2236 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2061 Ų buried · 19 hydrogen bonds · protein-protein
- C–A · 152 Ų buried · 0 hydrogen bonds · protein-protein
- D–A · 19 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 1SZR · A Dimer interface mutant of ornithine decarboxylase reveals structure of gem diamine… · the same entry in another collection · chain B against B, TM-score 1.00
- P07805 · AlphaFold monomer V2.0 prediction for ornithine decarboxylase (P07805) · a predicted model of the same protein · chain A 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 P07805
- Elsewhere: RCSB PDB 1SZR · PDBe 1SZR · UniProt P07805
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.