MolNFT v1 · #114727 · protein + DNA
X-ray structure of AAV2 obd-AAVS1 complex 2:1
5BYG · Protein REP78: “X-ray structure of AAV2 obd-AAVS1 complex 2:1”. X-ray diffraction, 1 ligand (MG), 11 pockets (best druggability 0.44). MolNFT v1 #114727 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5BYG
- Type
- protein + DNA
- Length
- 839 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein REP78; DNA (5'- D(*CP*TP*CP*GP*GP*CP*GP*CP*TP*CP*GP*CP*TP*CP*GP*CP*TP*CP*GP*CP*T)…
- UniProt
- Q89268
- Ligands
- MG
- Pockets
- 11 · best druggability 0.44
Structure
x-ray diffraction · 6 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein REP78 | protein | 181 | 39% helix, 19% strand | Q89268 |
| B | Protein REP78 | protein | 201 | 37% helix, 17% strand | Q89268 |
| C | Protein REP78 | protein | 193 | 37% helix, 18% strand | Q89268 |
| D | Protein REP78 | protein | 180 | 42% helix, 18% strand | Q89268 |
| E, G | DNA (5'- D(*CP*TP*CP*GP*GP*CP*GP*CP*TP*CP*GP*CP*TP*CP*GP*CP*TP*CP*GP*CP*T)- 3') | dna | 21 | — | — |
| F, H | DNA (5'- D(*GP*AP*GP*CP*GP*AP*GP*CP*GP*AP*GP*CP*GP*AP*GP*CP*GP*CP*CP*GP*A)- 3') | dna | 21 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- CIT · Citric acid · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.44 | 0.77 | 13 | empty |
| 2 | 84 | 0.43 | 0.79 | 21 | empty |
| 3 | 125 | 0.43 | 0.77 | 13 | empty |
| 4 | 127 | 0.39 | 0.75 | 20 | empty |
| 5 | 122 | 0.39 | 0.75 | 20 | empty |
Interfaces
10 interfaces between chains.
- G–H · 943 Ų buried · 99 hydrogen bonds · nucleic-nucleic
- E–F · 924 Ų buried · 92 hydrogen bonds · nucleic-nucleic
- A–E · 444 Ų buried · 10 hydrogen bonds · protein-nucleic
- D–G · 422 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–E · 410 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 5BYG · X-ray structure of AAV2 OBD-AAVS1 complex 2:1 · 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 Q89268
- Elsewhere: RCSB PDB 5BYG · PDBe 5BYG · UniProt Q89268
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