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Crystal structures of divalent metal dependent pyruvate aldolase, hpai, in complex with 4-hydroxyl-2-ketoheptane-1,7-dioate
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
- 4B5V
- 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
- PYR, E8U, 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
- PYR · Pyruvic acid · ligand · 2 copies · chains A, B
- E8U · (4R)-4-oxidanyl-2-oxidanylidene-heptanedioic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 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 | 125 | 0.54 | 0.82 | 25 | empty |
| 2 | 131 | 0.53 | 0.81 | 27 | empty |
| 3 | 159 | 0.45 | 0.76 | 27 | PYR, E8U, MG |
| 4 | 167 | 0.44 | 0.74 | 31 | PYR, E8U, MG |
Interfaces
1 interface between chains.
- A–B · 1371 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4B5V · 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 4B5V · PDBe 4B5V · UniProt B1IS70
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