MolNFT v1 · #174972 · protein
Crystal structure of white spot syndrome virus thymidylate synthase - ternary complex with methotrexate and dump
7CCA: “Crystal structure of white spot syndrome virus thymidylate synthase - ternary complex with methotrexate and…”. X-ray diffraction, 2 ligands (UMP, MTX), 5 pockets (best druggability 0.77). MolNFT v1 #174972 on GenesisL1: 3D…
- PDB
- 7CCA
- Type
- protein
- Length
- 576 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- UniProt
- Q77J90
- Ligands
- UMP, MTX
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase | protein | 289 | 35% helix, 22% strand | Q77J90 |
| B | Thymidylate synthase | protein | 287 | 35% helix, 23% strand | Q77J90 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 2 copies · chains A, B
- MTX · Methotrexate · ligand · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 528 | 0.77 | 0.84 | 48 | UMP, MTX |
| 2 | 546 | 0.77 | 0.84 | 42 | UMP, MTX |
| 3 | 383 | 0.59 | 0.76 | 53 | empty |
| 4 | 168 | 0.48 | 0.76 | 16 | empty |
| 5 | 154 | 0.48 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2042 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 7CCA · Crystal structure of White Spot Syndrome Virus Thymidylate Synthase - ternary complex… · the same entry in another collection · chain B against B, 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 Q77J90
- Elsewhere: RCSB PDB 7CCA · PDBe 7CCA · UniProt Q77J90
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