MolNFT v1 · #70212 · protein
1.77 ångström resolution crystal structure of orotidine 5'-phosphate decarboxylase from vibrio cholerae O1 biovar eltor str. N16961
3LDV: “1.77 ångström resolution crystal structure of orotidine 5'-phosphate decarboxylase from vibrio cholerae O1…”. X-ray diffraction, 2 ligands (MG, CL), 3 pockets (best druggability 0.77). MolNFT v1 #70212 on GenesisL1: 3D structure…
- PDB
- 3LDV
- Type
- protein
- Length
- 455 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotidine 5'-phosphate decarboxylase
- EC
- 4.1.1.23
- UniProt
- Q9KQT7
- Ligands
- MG, CL
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 231 | 49% helix, 17% strand | Q9KQT7 |
| B | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 224 | 49% helix, 17% strand | Q9KQT7 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.77 | 0.98 | 25 | empty |
| 2 | 401 | 0.65 | 0.79 | 50 | empty |
| 3 | 383 | 0.65 | 0.79 | 49 | empty |
Interfaces
1 interface between chains.
- A–B · 1794 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3LDV · 1.77 Angstrom resolution crystal structure of orotidine 5'-phosphate decarboxylase from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KQT7 · AlphaFold monomer V2.0 prediction for orotidine 5'-phosphate decarboxylase (Q9KQT7) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q9KQT7
- Elsewhere: RCSB PDB 3LDV · PDBe 3LDV · UniProt Q9KQT7
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