MolNFT v1 · #82035 · protein
1.7 ångström resolution crystal structure of shikimate kinase from bacteroides thetaiotaomicron
3VAA: “1.7 ångström resolution crystal structure of shikimate kinase from bacteroides thetaiotaomicron”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.65). MolNFT v1 #82035 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3VAA
- Type
- protein
- Length
- 521 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shikimate kinase
- EC
- 2.7.1.71
- UniProt
- Q8A2B2
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Shikimate kinase (EC 2.7.1.71) | protein | 176 | 60% helix, 13% strand | Q8A2B2 |
| C | Shikimate kinase (EC 2.7.1.71) | protein | 169 | 59% helix, 13% strand | Q8A2B2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains C
- BME · Beta-mercaptoethanol · additive · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 455 | 0.65 | 0.78 | 43 | GOL |
| 2 | 295 | 0.53 | 0.75 | 34 | PEG |
| 3 | 84 | 0.47 | 0.81 | 13 | empty |
| 4 | 203 | 0.46 | 0.74 | 27 | SO4 |
| 5 | 71 | 0.42 | 0.80 | 14 | empty |
Interfaces
2 interfaces between chains.
- B–C · 563 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 547 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (additive adduct).
Compared structures
- 3VAA · 1.7 Angstrom Resolution Crystal Structure of Shikimate Kinase from Bacteroides… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8A2B2 · AlphaFold monomer V2.0 prediction for shikimate kinase (Q8A2B2) · a predicted model of the same protein · chain C 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 Q8A2B2
- Elsewhere: RCSB PDB 3VAA · PDBe 3VAA · UniProt Q8A2B2
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