MolNFT v1 · #154325 · protein
Crystal structure of thymidylate synthase from shrimp
6K7Q: “Crystal structure of thymidylate synthase from shrimp”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.79). MolNFT v1 #154325 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6K7Q
- Type
- protein
- Length
- 4,215 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- C6GJB8
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 16 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 272 | 33% helix, 25% strand | C6GJB8 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 264 | 34% helix, 25% strand | C6GJB8 |
| C | Thymidylate synthase (EC 2.1.1.45) | protein | 267 | 34% helix, 25% strand | C6GJB8 |
| D | Thymidylate synthase (EC 2.1.1.45) | protein | 261 | 33% helix, 26% strand | C6GJB8 |
| E | Thymidylate synthase (EC 2.1.1.45) | protein | 260 | 33% helix, 25% strand | C6GJB8 |
| F | Thymidylate synthase (EC 2.1.1.45) | protein | 263 | 33% helix, 25% strand | C6GJB8 |
| G | Thymidylate synthase (EC 2.1.1.45) | protein | 255 | 34% helix, 24% strand | C6GJB8 |
| H | Thymidylate synthase (EC 2.1.1.45) | protein | 266 | 32% helix, 25% strand | C6GJB8 |
| I | Thymidylate synthase (EC 2.1.1.45) | protein | 267 | 33% helix, 25% strand | C6GJB8 |
| J | Thymidylate synthase (EC 2.1.1.45) | protein | 268 | 34% helix, 25% strand | C6GJB8 |
| K | Thymidylate synthase (EC 2.1.1.45) | protein | 261 | 35% helix, 24% strand | C6GJB8 |
| L | Thymidylate synthase (EC 2.1.1.45) | protein | 262 | 34% helix, 25% strand | C6GJB8 |
| M | Thymidylate synthase (EC 2.1.1.45) | protein | 263 | 34% helix, 25% strand | C6GJB8 |
| N | Thymidylate synthase (EC 2.1.1.45) | protein | 263 | 33% helix, 25% strand | C6GJB8 |
| O | Thymidylate synthase (EC 2.1.1.45) | protein | 262 | 34% helix, 25% strand | C6GJB8 |
| P | Thymidylate synthase (EC 2.1.1.45) | protein | 261 | 33% helix, 24% strand | C6GJB8 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 18 copies · chains A, B, C, F, D, E, G, H, I, J, K, L, M, N, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.79 | 0.81 | 81 | empty |
| 2 | 1032 | 0.77 | 0.80 | 84 | empty |
| 3 | 1149 | 0.77 | 0.79 | 95 | empty |
| 4 | 918 | 0.76 | 0.79 | 78 | empty |
| 5 | 999 | 0.74 | 0.77 | 93 | SO4 |
Interfaces
37 interfaces between chains.
- A–B · 1991 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 1977 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 1976 Ų buried · 31 hydrogen bonds · protein-protein
- I–J · 1975 Ų buried · 31 hydrogen bonds · protein-protein
- G–H · 1971 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 6K7Q · Crystal structure of thymidylate synthase from shrimp · 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 C6GJB8
- Elsewhere: RCSB PDB 6K7Q · PDBe 6K7Q · UniProt C6GJB8
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