Research workbench
1.90 ångström resolution crystal structure of N-terminal domain 3- phosphoshikimate 1-carboxyvinyltransferase from vibrio cholerae
Analyse 1.90 ångström resolution crystal structure of N-terminal domain 3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TI2
- Type
- protein
- Length
- 906 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
- Q9KRB0
- Ligands
- CL
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) | protein | 227 | 33% helix, 26% strand | Q9KRB0 |
| B | 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) | protein | 225 | 33% helix, 26% strand | Q9KRB0 |
| C | 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) | protein | 228 | 33% helix, 25% strand | Q9KRB0 |
| D | 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) | protein | 226 | 33% helix, 25% strand | Q9KRB0 |
Ligands and binding sites
- CL · Chloride ion · ion · 11 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · 2 copies · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.60 | 0.77 | 52 | CL |
| 2 | 299 | 0.57 | 0.77 | 46 | CL |
| 3 | 96 | 0.37 | 0.75 | 15 | empty |
| 4 | 99 | 0.36 | 0.74 | 14 | empty |
| 5 | 69 | 0.29 | 0.74 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 600 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 563 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 562 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3TI2 · 1.90 Angstrom resolution crystal structure of N-terminal domain 3-phosphoshikimate… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9KRB0 · AlphaFold monomer V2.0 prediction for 3-phosphoshikimate 1-carboxyvinyltransferase… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q9KRB0
- Elsewhere: RCSB PDB 3TI2 · PDBe 3TI2 · UniProt Q9KRB0
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