MolNFT v1 · #60480 · protein
Crystal structure of a putative aminoglycoside phosphotransferase (YP_614837.1) from silicibacter sp. TM1040 at 2.15 a resolution
3CSV: “Crystal structure of a putative aminoglycoside phosphotransferase (YP_614837.1) from silicibacter sp. TM1040…”. X-ray diffraction, 4 ligands (ZN, NA, CL), 3 pockets (best druggability 0.56). MolNFT v1 #60480 on GenesisL1: 3D…
- PDB
- 3CSV
- Type
- protein
- Length
- 322 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminoglycoside phosphotransferase
- UniProt
- Q1GCP1
- Ligands
- ZN, NA, CL, SO4
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminoglycoside phosphotransferase | protein | 322 | 56% helix, 11% strand | Q1GCP1 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 11 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.56 | 0.83 | 23 | EDO |
| 2 | 148 | 0.49 | 0.78 | 19 | CL |
| 3 | 66 | 0.30 | 0.74 | 13 | EDO |
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 3CSV · Crystal structure of a putative aminoglycoside phosphotransferase (YP_614837.1) 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 Q1GCP1
- Elsewhere: RCSB PDB 3CSV · PDBe 3CSV · UniProt Q1GCP1
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