MolNFT v1 · #64374 · protein
Crystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 5,6- dihydrouridine 5'-monophosphate
3G1H · Orotidine 5'-phosphate decarboxylase: “Crystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum…”. X-ray diffraction, 1 ligand (H2U), 20 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 3G1H
- Type
- protein
- Length
- 2,816 residues
- Chains
- 13
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotidine 5'-phosphate decarboxylase
- EC
- 4.1.1.23
- UniProt
- O26232
- Ligands
- H2U
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 221 | 49% helix, 19% strand | O26232 |
| B, H, K, L | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 216 | 46% helix, 19% strand | O26232 |
| C, J | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 218 | 50% helix, 19% strand | O26232 |
| D | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 215 | 49% helix, 19% strand | O26232 |
| E, F, G, M | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 217 | 48% helix, 19% strand | O26232 |
| I | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 212 | 47% helix, 20% strand | O26232 |
Ligands and binding sites
- H2U · 5,6-dihydrouridine-5'-monophosphate · ligand · 13 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.86 | 0.96 | 70 | H2U |
| 2 | 305 | 0.86 | 0.97 | 74 | H2U |
| 3 | 297 | 0.86 | 0.96 | 71 | H2U |
| 4 | 374 | 0.86 | 0.95 | 79 | H2U |
| 5 | 322 | 0.86 | 0.95 | 77 | H2U |
Interfaces
13 interfaces between chains.
- C–D · 1711 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1708 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1704 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 1690 Ų buried · 14 hydrogen bonds · protein-protein
- I–J · 1663 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3G1H · Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium… · 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 O26232
- Elsewhere: RCSB PDB 3G1H · PDBe 3G1H · UniProt O26232
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