MolNFT v1 · #146794 · protein
Re-refinement of P. falciparum orotidine 5'-monophosphate decarboxylase
6DSS: “Re-refinement of P. falciparum orotidine 5'-monophosphate decarboxylase”. X-ray diffraction, 1 ligand (U5P), 7 pockets (best druggability 0.79). MolNFT v1 #146794 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6DSS
- Type
- protein
- Length
- 638 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotidine 5'-monophosphate decarboxylase
- EC
- 4.1.1.23
- UniProt
- Q8T6J6
- Ligands
- U5P
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotidine 5'-monophosphate decarboxylase (EC 4.1.1.23) | protein | 320 | 55% helix, 15% strand | Q8T6J6 |
| B | Orotidine 5'-monophosphate decarboxylase (EC 4.1.1.23) | protein | 318 | 54% helix, 15% strand | Q8T6J6 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.79 | 0.97 | 33 | U5P |
| 2 | 110 | 0.75 | 0.96 | 32 | U5P |
| 3 | 113 | 0.40 | 0.76 | 14 | empty |
| 4 | 68 | 0.36 | 0.78 | 15 | empty |
| 5 | 71 | 0.35 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2533 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 6DSS · Re-refinement of P. falciparum orotidine 5'-monophosphate decarboxylase · the same entry in another collection · chain A 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 Q8T6J6
- Elsewhere: RCSB PDB 6DSS · PDBe 6DSS · UniProt Q8T6J6
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