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Crystal structure of Thymidylate Synthase Complementing Protein (TM0449) from Thermotoga maritima with FAD and FdUMP at 2.0 A resolution
Analyse Crystal structure of Thymidylate Synthase Complementing Protein (TM0449) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1O29
- Type
- protein
- Length
- 867 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Thermotoga maritima
- Molecule
- Thymidylate synthase thyX
- EC
- 2.1.1.-
- UniProt
- Q9WYT0
- Ligands
- UFP, FAD
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · resolution 2 · 4 distinct chains · 51% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase thyX (EC 2.1.1.-) | protein | 216 | 52% 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 | 48% helix, 18% strand | Q9WYT0 |
| D | Thymidylate synthase thyX (EC 2.1.1.-) | protein | 215 | 53% helix, 18% strand | Q9WYT0 |
Ligands and binding sites
- UFP · 5-fluoro-2'-deoxyuridine-5'-monophosphate · ligand · 4 copies · chains A, D, B, C
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.82 | 0.92 | 39 | empty |
| 2 | 421 | 0.81 | 0.89 | 43 | UFP, FAD |
| 3 | 224 | 0.79 | 0.93 | 30 | UFP, FAD |
| 4 | 196 | 0.78 | 0.93 | 31 | FAD, UFP |
| 5 | 128 | 0.72 | 0.92 | 28 | UFP |
Interfaces
6 interfaces between chains.
- B–C · 2241 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 2210 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 1425 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1243 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 254 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1O29 · Crystal structure of thymidylate synthase complementing protein (TM0449) from thermotoga… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9WYT0 · AlphaFold monomer V2.0 prediction for flavin-dependent thymidylate synthase (Q9WYT0) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 1O29 · PDBe 1O29 · UniProt Q9WYT0
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