MolNFT v1 · #16544 · protein
Crystal structure of thymidylate synthase complementing protein (TM0449) from thermotoga maritima with fdump at 2.1 a resolution
1O28 · Thymidylate synthase thyx: “Crystal structure of thymidylate synthase complementing protein (TM0449) from thermotoga maritima with fdump…”. X-ray diffraction, 1 ligand (UFP), 6 pockets (best druggability 0.88). MolNFT v1 #16544 on…
- PDB
- 1O28
- Type
- protein
- Length
- 868 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase thyx
- EC
- 2.1.1.-
- UniProt
- Q9WYT0
- Ligands
- UFP
- Pockets
- 6 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase thyx (EC 2.1.1.-) | protein | 218 | 50% helix, 18% strand | Q9WYT0 |
| B | Thymidylate synthase thyx (EC 2.1.1.-) | protein | 220 | 52% helix, 17% strand | Q9WYT0 |
| C | Thymidylate synthase thyx (EC 2.1.1.-) | protein | 216 | 51% helix, 18% strand | Q9WYT0 |
| D | Thymidylate synthase thyx (EC 2.1.1.-) | protein | 214 | 52% helix, 18% strand | Q9WYT0 |
Ligands and binding sites
- UFP · 5-fluoro-2'-deoxyuridine-5'-monophosphate · ligand · 4 copies · chains A, D, B, C
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, C, B, D
- PGE · Triethylene glycol · additive · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 879 | 0.88 | 0.90 | 90 | EPE, PGE, UFP |
| 2 | 351 | 0.81 | 0.91 | 40 | UFP, EPE |
| 3 | 334 | 0.81 | 0.91 | 41 | UFP, EPE |
| 4 | 222 | 0.75 | 0.90 | 30 | EPE, UFP |
| 5 | 56 | 0.51 | 0.87 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2234 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2224 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1396 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1163 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 245 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1O28 · Crystal structure of Thymidylate Synthase Complementing Protein (TM0449) from Thermotoga… · 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 Q9WYT0
- Elsewhere: RCSB PDB 1O28 · PDBe 1O28 · UniProt Q9WYT0
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