Research workbench
Crystal structures of divalent metal dependent pyruvate aldolase R70A mutant, hpai, in complex with pyruvate
Analyse Crystal structures of divalent metal dependent pyruvate aldolase R70A mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.