MolNFT v1 · #97360 · protein
Crystal structure of probable sugar kinase protein from rhizobium etli cfn 42 complexed with benzoguanamine
4KBE: “Crystal structure of probable sugar kinase protein from rhizobium etli cfn 42 complexed with benzoguanamine”. X-ray diffraction, 3 ligands (ADN, BZE, K), 6 pockets (best druggability 0.77). MolNFT v1 #97360 on GenesisL1: 3D…
- PDB
- 4KBE
- Type
- protein
- Length
- 660 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable sugar kinase protein
- UniProt
- Q2KDX6
- Ligands
- ADN, BZE, K
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable sugar kinase protein | protein | 330 | 44% helix, 22% strand | Q2KDX6 |
Ligands and binding sites
- ADN · Adenosine · ligand · 2 copies · chains A, B
- BZE · 6-phenyl-1,3,5-triazine-2,4-diamine · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.77 | 0.86 | 56 | ADN |
| 2 | 427 | 0.76 | 0.85 | 61 | ADN |
| 3 | 489 | 0.65 | 0.77 | 42 | BZE, DMS |
| 4 | 166 | 0.64 | 0.86 | 26 | DMS, BZE |
| 5 | 107 | 0.51 | 0.82 | 16 | DMS |
Interfaces
1 interface between chains.
- A–B · 957 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 4KBE · Crystal structure of probable sugar kinase protein from Rhizobium etli CFN 42 complexed… · 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 Q2KDX6
- Elsewhere: RCSB PDB 4KBE · PDBe 4KBE · UniProt Q2KDX6
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