Research workbench
Crystal structures of divalent metal dependent pyruvate aldolase, hpai, in complex with ketobutyrate
Analyse Crystal structures of divalent metal dependent pyruvate aldolase, hpai, in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B5T
- Type
- protein
- Length
- 502 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-2-oxo-heptane-1,7-dioate aldolase
- EC
- 4.1.2.20
- UniProt
- B1IS70
- Ligands
- 2KT, CO, MG
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 4-hydroxy-2-oxo-heptane-1,7-dioate aldolase (EC 4.1.2.20) | protein | 251 | 46% helix, 17% strand | B1IS70 |
Ligands and binding sites
- 2KT · 2-ketobutyric acid · ligand · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.54 | 0.83 | 23 | empty |
| 2 | 132 | 0.53 | 0.81 | 27 | empty |
| 3 | 156 | 0.45 | 0.75 | 25 | CO, MG, 2KT |
| 4 | 172 | 0.44 | 0.74 | 30 | CO, MG, 2KT |
Interfaces
1 interface between chains.
- A–B · 1374 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4B5T · Crystal structures of divalent metal dependent pyruvate aldolase, HpaI, in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- B1IS70 · AlphaFold monomer V2.0 prediction for 4-hydroxy-2-oxo- heptane-1,7-dioate aldolase… · 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 B1IS70
- Elsewhere: RCSB PDB 4B5T · PDBe 4B5T · UniProt B1IS70
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