Research workbench
Crystal structure of burkholderia cenocepacia hlda in complex with an ATP-competitive inhibitor
Analyse Crystal structure of burkholderia cenocepacia hlda in complex with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E8Y
- Type
- protein
- Length
- 615 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
- IHA, M7B, K, CL, PO4
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-beta-D-heptose 7-phosphate kinase | protein | 308 | 35% helix, 30% strand | B4EB35 |
| B | D-beta-D-heptose 7-phosphate kinase | protein | 307 | 36% helix, 31% strand | B4EB35 |
Ligands and binding sites
- IHA · {[2-({[5-(2,6-dimethoxyphenyl)-1,2,4-triazin-3-yl]amino}methyl)-1,3-benzothiazol-5-yl]oxy}acetic acid · ligand · 2 copies · chains A, B
- M7B · 7-O-phosphono-D-glycero-beta-D-manno-heptopyranose · ligand · chains A
- K · Potassium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.71 | 0.97 | 30 | empty |
| 2 | 300 | 0.62 | 0.80 | 41 | IHA, M7B |
| 3 | 359 | 0.62 | 0.78 | 49 | IHA, PO4 |
Compared structures
- 4E8Y · Crystal Structure of Burkholderia cenocepacia HldA in Complex with an ATP-competitive… · 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 4E8Y · PDBe 4E8Y · UniProt B4EB35
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