MolNFT v1 · #103075 · protein
Crystal structure of a UMP/DUMP methylase polb from streptomyces cacaoi bound with 5-br dump
4P5B · Thymidylate synthase thyx: “Crystal structure of a UMP/DUMP methylase polb from streptomyces cacaoi bound with 5-br dump”. X-ray diffraction, 3 ligands (FAD, BRU, SO4), 11 pockets (best druggability 0.88). MolNFT v1 #103075 on…
- PDB
- 4P5B
- Type
- protein
- Length
- 933 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, BRU, SO4
- Pockets
- 11 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 229 | 48% helix, 16% strand | C1IC19 |
| B, D | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 235 | 52% helix, 17% strand | C1IC19 |
| C | Thymidylate synthase thyx (EC 2.1.1.148) | protein | 234 | 50% helix, 17% strand | C1IC19 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- BRU · 5-bromo-2'-deoxyuridine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.88 | 0.93 | 91 | FAD, BRU |
| 2 | 540 | 0.86 | 0.93 | 91 | FAD, BRU |
| 3 | 115 | 0.70 | 0.93 | 28 | empty |
| 4 | 115 | 0.69 | 0.92 | 24 | empty |
| 5 | 71 | 0.60 | 0.91 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2473 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2423 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 1568 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 1557 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 606 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4P5B · 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 4P5B · PDBe 4P5B · UniProt C1IC19
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