MolNFT v1 · #86413 · protein
Crystal structures of divalent metal dependent pyruvate aldolase R70A mutant, hpai, in complex with pyruvate
4B5W · 4-hydroxy-2-oxo-heptane-1,7-dioate aldolase: “Crystal structures of divalent metal dependent pyruvate aldolase R70A mutant, hpai, in complex with pyruvate”. X-ray diffraction, 3 ligands (PYR, CO, CA), 20 pockets (best druggability…
- PDB
- 4B5W
- Type
- protein
- Length
- 1,523 residues
- Chains
- 6
- 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, CO, CA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxy-2-oxo-heptane-1,7-dioate aldolase (EC 4.1.2.20) | protein | 256 | 45% helix, 17% strand | B1IS70 |
| B, D | 4-hydroxy-2-oxo-heptane-1,7-dioate aldolase (EC 4.1.2.20) | protein | 253 | 46% helix, 17% strand | B1IS70 |
| C | 4-hydroxy-2-oxo-heptane-1,7-dioate aldolase (EC 4.1.2.20) | protein | 252 | 45% helix, 17% strand | B1IS70 |
| E | 4-hydroxy-2-oxo-heptane-1,7-dioate aldolase (EC 4.1.2.20) | protein | 255 | 45% helix, 17% strand | B1IS70 |
| F | 4-hydroxy-2-oxo-heptane-1,7-dioate aldolase (EC 4.1.2.20) | protein | 254 | 46% helix, 17% strand | B1IS70 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 6 copies · chains A, B, C, D, E, F
- CO · Cobalt (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 5 copies · chains A, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.80 | 0.86 | 62 | empty |
| 2 | 589 | 0.79 | 0.85 | 60 | empty |
| 3 | 1166 | 0.78 | 0.80 | 80 | empty |
| 4 | 351 | 0.71 | 0.83 | 46 | PYR |
| 5 | 363 | 0.71 | 0.83 | 45 | CO, PYR |
Interfaces
12 interfaces between chains.
- A–D · 1552 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 1476 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 1364 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 905 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 902 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4B5W · Crystal structures of divalent metal dependent pyruvate aldolase R70A mutant, HpaI, in… · the same entry in another collection · chain F against F, 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 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 B1IS70
- Elsewhere: RCSB PDB 4B5W · PDBe 4B5W · UniProt B1IS70
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