MolNFT v1 · #25982 · protein
Crystal structure of the E45N mutant from kdpg aldolase from escherichia COLI
1WBH · KHG/KDPG aldolase: “Crystal structure of the E45N mutant from kdpg aldolase from escherichia COLI”. X-ray diffraction, 1 ligand (PO4), 8 pockets (best druggability 0.76). MolNFT v1 #25982 on GenesisL1: 3D structure, binding sites…
- PDB
- 1WBH
- Type
- protein
- Length
- 640 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- KHG/KDPG aldolase
- EC
- 4.1.2.14
- UniProt
- P10177
- Ligands
- PO4
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | KHG/KDPG aldolase (EC 4.1.2.14) | protein | 213 | 45% helix, 17% strand | P10177 |
| B | KHG/KDPG aldolase (EC 4.1.2.14) | protein | 214 | 43% helix, 17% strand | P10177 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C
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 | 203 | 0.76 | 0.91 | 28 | empty |
| 2 | 110 | 0.69 | 0.91 | 27 | empty |
| 3 | 84 | 0.42 | 0.79 | 29 | PO4 |
| 4 | 95 | 0.40 | 0.77 | 18 | PO4 |
| 5 | 98 | 0.36 | 0.75 | 20 | PO4 |
Interfaces
3 interfaces between chains.
- B–C · 600 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 599 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 588 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1WBH · Crystal structure of the E45N mutant from KDPG aldolase from Escherichia coli · 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 P10177
- Elsewhere: RCSB PDB 1WBH · PDBe 1WBH · UniProt P10177
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