Research workbench
DNA substrate selection by APOBEC3G
Analyse DNA substrate selection by APOBEC3G in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BWY
- Type
- protein + DNA
- Length
- 1,410 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (30-mer); Protection of telomeres protein 1, DNA dc->
- EC
- 3.5.4.-
- UniProt
- O13988, Q9HC16
- Ligands
- ZN, PO4
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I, C, D, F | DNA (30-mer) | dna | 7 | — | — |
| A | Protection of telomeres protein 1, DNA dc-> (EC 3.5.4.-) | protein | 344 | 24% helix, 32% strand | O13988, Q9HC16 |
| B, E, G | Protection of telomeres protein 1, DNA dc-> (EC 3.5.4.-) | protein | 346 | 26% helix, 32% strand | O13988, Q9HC16 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, E, G
- PO4 · Phosphate ion · ion · 15 copies · chains I, C, G, D, F, A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.72 | 0.86 | 41 | empty |
| 2 | 833 | 0.69 | 0.75 | 67 | empty |
| 3 | 776 | 0.68 | 0.75 | 48 | PO4 |
| 4 | 192 | 0.57 | 0.81 | 32 | empty |
| 5 | 258 | 0.52 | 0.75 | 33 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1248 Ų buried · 16 hydrogen bonds · protein-protein
- E–G · 706 Ų buried · 11 hydrogen bonds · protein-protein
- I–A · 681 Ų buried · 29 hydrogen bonds · protein-nucleic
- F–E · 670 Ų buried · 27 hydrogen bonds · protein-nucleic
- C–G · 659 Ų buried · 25 hydrogen bonds · protein-nucleic
Compared structures
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 O13988
- Every structure of UniProt Q9HC16
- Elsewhere: RCSB PDB 6BWY · PDBe 6BWY · UniProt O13988 · UniProt Q9HC16
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