MolNFT v1 · #169416 · protein + DNA
Adeno-associated virus origin binding domain in complex with ssdna
6XB8 · Protein REP68: “Adeno-associated virus origin binding domain in complex with ssdna”. X-ray diffraction, 1 ligand (ZN), 9 pockets (best druggability 0.60). MolNFT v1 #169416 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6XB8
- Type
- protein + DNA
- Length
- 817 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein REP68; DNA (5'-D(*GP*CP*TP*CP*TP*T)-3')
- EC
- 3.6.4.12
- UniProt
- P03132
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.60
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein REP68 (EC 3.6.4.12) | protein | 205 | 41% helix, 17% strand | P03132 |
| B | Protein REP68 (EC 3.6.4.12) | protein | 200 | 41% helix, 18% strand | P03132 |
| C | Protein REP68 (EC 3.6.4.12) | protein | 206 | 42% helix, 17% strand | P03132 |
| D | Protein REP68 (EC 3.6.4.12) | protein | 196 | 40% helix, 18% strand | P03132 |
| E | DNA (5'-D(*GP*CP*TP*CP*TP*T)-3') | dna | 6 | — | — |
| F | DNA (5'-D(*GP*CP*TP*CP*TP*T)-3') | dna | 4 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 424 | 0.60 | 0.76 | 51 | empty |
| 2 | 255 | 0.56 | 0.78 | 34 | empty |
| 3 | 192 | 0.54 | 0.79 | 27 | empty |
| 4 | 195 | 0.53 | 0.78 | 23 | empty |
| 5 | 109 | 0.36 | 0.74 | 17 | empty |
Interfaces
8 interfaces between chains.
- A–B · 627 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 625 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 488 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–E · 474 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–F · 363 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 6XB8 · Adeno-Associated Virus Origin Binding Domain in complex with ssDNA · 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 P03132
- Elsewhere: RCSB PDB 6XB8 · PDBe 6XB8 · UniProt P03132
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