MolNFT v1 · #137220 · protein + DNA
Pseudomonas fluorescens alkylpurine DNA glycosylase alkc bound to DNA containing an oxocarbenium-intermediate analog
5VHV: “Pseudomonas fluorescens alkylpurine DNA glycosylase alkc bound to DNA containing an oxocarbenium-intermediate…”. X-ray diffraction, 2 ligands (9B4, NA). MolNFT v1 #137220 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VHV
- Type
- protein + DNA
- Length
- 766 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- C3K795
- Ligands
- 9B4, NA
Structure
x-ray diffraction · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | — | protein | 361 | — | C3K795 |
| C, E | — | dna | 11 | — | — |
| D, F | — | dna | 11 | — | — |
Ligands and binding sites
- 9B4 · (2R,5R,13R,16R)-9-(hydroxymethyl)-9-{[(2R)-2-hydroxypropoxy]methyl}-5,13-dimethyl-4,7,11,14-tetraoxaheptadecane-2,16-diol · ligand · 2 copies · chains A, C, D, B, E, F
- NA · Sodium ion · metal · 2 copies · chains C, D, E, F
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, D, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 5VHV · Pseudomonas fluorescens alkylpurine DNA glycosylase AlkC bound to DNA containing an… · 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 C3K795
- Elsewhere: RCSB PDB 5VHV · PDBe 5VHV · UniProt C3K795
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