MolNFT v1 · #177771 · protein
Crystal structure of abhpai-zn-(4S)-kdglu complex, class II aldolase, hpai from acinetobacter baumannii
7ETD · 4-hydroxy-2-oxoheptanedioate aldolase: “Crystal structure of abhpai-zn-(4S)-kdglu complex, class II aldolase, hpai from acinetobacter baumannii”. X-ray diffraction, 3 ligands (KDG, ZN, CA), 13 pockets (best druggability 0.80).…
- PDB
- 7ETD
- 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
- KDG, ZN, CA
- Pockets
- 13 · best druggability 0.80
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
- KDG · 2-keto-3-deoxygluconate · ligand · 3 copies · chains A, C, B
- 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.80 | 0.87 | 46 | empty |
| 2 | 333 | 0.69 | 0.82 | 45 | KDG, ZN |
| 3 | 336 | 0.67 | 0.81 | 44 | KDG, ZN |
| 4 | 340 | 0.66 | 0.81 | 43 | KDG, ZN |
| 5 | 113 | 0.61 | 0.87 | 24 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1053 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1048 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1047 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7ETD · Crystal structure of AbHpaI-Zn-(4S)-KDGlu 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 7ETD · PDBe 7ETD · UniProt A0A5R9HKL3
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