MolNFT v1 · #188319 · protein
Crystal structure of shikimate-3-phosphate and glyphosate bound 3- phosphoshikimate 1-carboxyvinyltransferase from klebsiella pneumoniae
7TM6 · 3-phosphoshikimate 1-carboxyvinyltransferase: “Crystal structure of shikimate-3-phosphate and glyphosate bound 3- phosphoshikimate 1-carboxyvinyltransferase…”. X-ray diffraction, 2 ligands (S3P, GPJ), 5 pockets (best druggability…
- PDB
- 7TM6
- Type
- protein
- Length
- 853 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-phosphoshikimate 1-carboxyvinyltransferase
- EC
- 2.5.1.19
- UniProt
- A0A0H3GV01
- Ligands
- S3P, GPJ
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) | protein | 426 | 36% helix, 26% strand | A0A0H3GV01 |
| B | 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) | protein | 427 | 35% helix, 27% strand | A0A0H3GV01 |
Ligands and binding sites
- S3P · Shikimate-3-phosphate · ligand · 2 copies · chains A, B
- GPJ · Glyphosate · ligand · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 3 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 | 94 | 0.75 | 0.97 | 30 | S3P, GPJ |
| 2 | 76 | 0.72 | 0.97 | 28 | S3P, GPJ |
| 3 | 362 | 0.53 | 0.73 | 47 | empty |
| 4 | 60 | 0.30 | 0.75 | 13 | empty |
| 5 | 55 | 0.28 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 178 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7TM6 · Crystal structure of shikimate-3-phosphate and glyphosate bound 3-phosphoshikimate… · 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 A0A0H3GV01
- Elsewhere: RCSB PDB 7TM6 · PDBe 7TM6 · UniProt A0A0H3GV01
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