MolNFT v1 · #90068 · protein
Crystal structure of burkholderia cenocepacia hlda
4E84 · D-beta-D-heptose 7-phosphate kinase: “Crystal structure of burkholderia cenocepacia hlda”. X-ray diffraction, 7 ligands (ANP, M7B, GMZ), 5 pockets (best druggability 0.70). MolNFT v1 #90068 on GenesisL1: 3D structure, binding sites…
- PDB
- 4E84
- Type
- protein
- Length
- 623 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-beta-D-heptose 7-phosphate kinase
- UniProt
- B4EB35
- Ligands
- ANP, M7B, GMZ, K, MG, CL, PO4
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-beta-D-heptose 7-phosphate kinase | protein | 313 | 35% helix, 29% strand | B4EB35 |
| B | D-beta-D-heptose 7-phosphate kinase | protein | 310 | 35% helix, 30% strand | B4EB35 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- M7B · 7-O-phosphono-D-glycero-beta-D-manno-heptopyranose · ligand · chains A, B
- GMZ · 1,7-di-O-phosphono-D-glycero-beta-D-manno-heptopyranose · ligand · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.70 | 0.98 | 18 | empty |
| 2 | 554 | 0.70 | 0.79 | 64 | ANP, M7B, MG |
| 3 | 425 | 0.69 | 0.81 | 46 | ANP, GMZ, MG |
| 4 | 258 | 0.52 | 0.75 | 32 | empty |
| 5 | 132 | 0.40 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1144 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 4E84 · Crystal Structure of Burkholderia cenocepacia HldA · 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 B4EB35
- Elsewhere: RCSB PDB 4E84 · PDBe 4E84 · UniProt B4EB35
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