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Crystal structure of a UMP/DUMP methylase polb from streptomyces cacaoi bound with 5-br ump
Analyse Crystal structure of a UMP/DUMP methylase polb from streptomyces cacaoi bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P5A
- Type
- protein
- Length
- 901 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase thyx
- EC
- 2.1.1.148
- UniProt
- C1IC19
- Ligands
- FAD, 5BU
- Pockets
- 9 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 226 | 46% helix, 19% strand | C1IC19 |
| B | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 227 | 46% helix, 19% strand | C1IC19 |
| C | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 223 | 47% helix, 19% strand | C1IC19 |
| D | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 225 | 46% helix, 19% strand | C1IC19 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- 5BU · 5-bromo-uridine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.89 | 0.92 | 126 | FAD, 5BU |
| 2 | 468 | 0.85 | 0.92 | 81 | FAD, 5BU |
| 3 | 70 | 0.65 | 0.93 | 17 | empty |
| 4 | 85 | 0.64 | 0.91 | 22 | empty |
| 5 | 57 | 0.63 | 0.93 | 20 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2689 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 2642 Ų buried · 40 hydrogen bonds · protein-protein
- A–D · 1256 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1197 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 713 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4P5A · Crystal structure of a UMP/dUMP methylase PolB from Streptomyces cacaoi bound with 5-Br… · 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 C1IC19
- Elsewhere: RCSB PDB 4P5A · PDBe 4P5A · UniProt C1IC19
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