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1.70 ångström resolution structure of 3-phosphoshikimate 1- carboxyvinyltransferase (aroa) from coxiella burnetii in complex with shikimate-3-phosphate and glyphosate
Analyse 1.70 ångström resolution structure of 3-phosphoshikimate 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SLH
- Type
- protein
- Length
- 1,753 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-phosphoshikimate 1-carboxyvinyltransferase
- EC
- 2.5.1.19
- UniProt
- Q83E11
- Ligands
- GPJ, S3P, SKM, PO4, CL
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) | protein | 436 | 36% helix, 28% strand | Q83E11 |
| B | 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) | protein | 439 | 35% helix, 27% strand | Q83E11 |
| C | 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) | protein | 438 | 35% helix, 27% strand | Q83E11 |
| D | 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) | protein | 440 | 35% helix, 28% strand | Q83E11 |
Ligands and binding sites
- GPJ · Glyphosate · ligand · 5 copies · chains A, B, C, D
- S3P · Shikimate-3-phosphate · ligand · 4 copies · chains A, B, C, D
- SKM · (3R,4S,5R)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C
- CL · Chloride ion · ion · 2 copies · chains C, D
- PEG · Di(hydroxyethyl)ether · additive · 14 copies · chains A, B, C, D
- BME · Beta-mercaptoethanol · additive · 5 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, C
- PG4 · Tetraethylene glycol · additive · 3 copies · chains C, A, D
- PGE · Triethylene glycol · additive · chains B
- 1PE · Pentaethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.80 | 0.81 | 104 | PO4, S3P, GPJ, SKM, PEG |
| 2 | 160 | 0.75 | 0.93 | 34 | GPJ, S3P, SKM |
| 3 | 145 | 0.74 | 0.93 | 35 | PO4, S3P, GPJ, SKM |
| 4 | 163 | 0.71 | 0.90 | 35 | PO4, GPJ, SKM, S3P |
| 5 | 615 | 0.69 | 0.78 | 61 | empty |
Interfaces
4 interfaces between chains.
- A–B · 596 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 554 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 292 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 280 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent, 4 disulfide (additive adduct, disulfide).
Compared structures
- 3SLH · 1.70 Angstrom resolution structure of 3-phosphoshikimate 1-carboxyvinyltransferase (AroA)… · the same entry in another collection · chain D against D, TM-score 1.00
- Q83E11 · AlphaFold monomer V2.0 prediction for 3-phosphoshikimate 1-carboxyvinyltransferase… · a predicted model of the same protein · chain A 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 Q83E11
- Elsewhere: RCSB PDB 3SLH · PDBe 3SLH · UniProt Q83E11
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