Research workbench
Crystal structure of a primate APOBEC3G N-domain, in complex with ssdna
Analyse Crystal structure of a primate APOBEC3G N-domain, in complex with ssdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K83
- Type
- protein + DNA
- Length
- 1,133 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apolipoprotein B mRNA editing enzyme, catalytic peptide- like 3G,APOLIPOPROTEIN B mRNA…
- UniProt
- M1GSK9
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, B | Apolipoprotein B mRNA editing enzyme, catalytic peptide- like 3G,APOLIPOPROTEIN B mRNA editing enzyme, catalytic peptide-like 3G | protein | 185 | 39% helix, 23% strand | M1GSK9 |
| C, E, A | Apolipoprotein B mRNA editing enzyme, catalytic peptide- like 3G,APOLIPOPROTEIN B mRNA editing enzyme, catalytic peptide-like 3G | protein | 191 | 41% helix, 20% strand | M1GSK9 |
| I, J, H | DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') | dna | 2 | — | — |
| F | Apolipoprotein B mRNA editing enzyme, catalytic peptide- like 3G,APOLIPOPROTEIN B mRNA editing enzyme, catalytic peptide-like 3G | protein | 184 | 40% helix, 23% strand | M1GSK9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains D, C, I, F, E, J, B, A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.76 | 0.78 | 77 | empty |
| 2 | 933 | 0.75 | 0.78 | 72 | empty |
| 3 | 60 | 0.41 | 0.81 | 13 | empty |
| 4 | 64 | 0.41 | 0.80 | 13 | empty |
| 5 | 55 | 0.40 | 0.81 | 14 | empty |
Interfaces
10 interfaces between chains.
- F–E · 729 Ų buried · 1 hydrogen bond · protein-protein
- B–A · 724 Ų buried · 1 hydrogen bond · protein-protein
- D–C · 716 Ų buried · 1 hydrogen bond · protein-protein
- D–B · 497 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 464 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5K83 · Crystal Structure of a Primate APOBEC3G N-Domain, in Complex with ssDNA · the same entry in another collection · chain D against D, 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 M1GSK9
- Elsewhere: RCSB PDB 5K83 · PDBe 5K83 · UniProt M1GSK9
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