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Crystal structure of abhpai-zn-(4R)-kdgal complex, class II aldolase, hpai from acinetobacter baumannii
Analyse Crystal structure of abhpai-zn-(4R)-kdgal complex, class II aldolase, hpai from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ETC
- Type
- protein
- Length
- 759 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-2-oxoheptanedioate aldolase
- EC
- 4.1.2.52
- UniProt
- A0A5R9HKL3
- Ligands
- PYR, JBU, ZN, CA
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 4-hydroxy-2-oxoheptanedioate aldolase (EC 4.1.2.52) | protein | 253 | 44% helix, 16% strand | A0A5R9HKL3 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 2 copies · chains A, B, C
- JBU · (4R,5R)-4,5,6-tris(oxidanyl)-2-oxidanylidene-hexanoic acid · ligand · chains A, C
- ZN · Zinc ion · metal · 3 copies · chains A, C, B
- CA · Calcium ion · metal · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.81 | 0.87 | 46 | empty |
| 2 | 332 | 0.67 | 0.81 | 46 | PYR |
| 3 | 332 | 0.66 | 0.81 | 46 | ZN, JBU |
| 4 | 323 | 0.65 | 0.81 | 46 | ZN, PYR |
| 5 | 119 | 0.62 | 0.87 | 24 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1057 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1047 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1047 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 7ETC · Crystal structure of AbHpaI-Zn-(4R)-KDGal complex, Class II aldolase, HpaI from… · 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 A0A5R9HKL3
- Elsewhere: RCSB PDB 7ETC · PDBe 7ETC · UniProt A0A5R9HKL3
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