MolNFT v1 · #112602 · protein + DNA
X-ray structure of aav-2 obd bound to AAVS1 site 3:1
4ZQ9 · Protein REP68: “X-ray structure of aav-2 obd bound to AAVS1 site 3:1”. X-ray diffraction, 1 ligand (MN), 8 pockets (best druggability 0.47). MolNFT v1 #112602 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4ZQ9
- Type
- protein + DNA
- Length
- 603 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein REP68; DNA (5'- D(*GP*CP*GP*CP*TP*CP*GP*CP*TP*CP*GP*CP*TP*CP*GP*CP*TP*GP*GP*GP*C)…
- EC
- 3.6.4.12
- UniProt
- P03132
- Ligands
- MN
- Pockets
- 8 · best druggability 0.47
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein REP68 (EC 3.6.4.12) | protein | 185 | 36% helix, 19% strand | P03132 |
| B | Protein REP68 (EC 3.6.4.12) | protein | 189 | 33% helix, 19% strand | P03132 |
| C | Protein REP68 (EC 3.6.4.12) | protein | 187 | 35% helix, 19% strand | P03132 |
| D | DNA (5'- D(*GP*CP*GP*CP*TP*CP*GP*CP*TP*CP*GP*CP*TP*CP*GP*CP*TP*GP*GP*GP*C)- 3') | dna | 21 | — | — |
| E | DNA (5'- D(*CP*GP*CP*CP*CP*AP*GP*CP*GP*AP*GP*CP*GP*AP*GP*CP*GP*AP*GP*CP*G)- 3') | dna | 21 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.47 | 0.81 | 20 | empty |
| 2 | 157 | 0.47 | 0.78 | 14 | empty |
| 3 | 143 | 0.45 | 0.77 | 14 | empty |
| 4 | 144 | 0.40 | 0.74 | 21 | empty |
| 5 | 113 | 0.38 | 0.75 | 17 | empty |
Interfaces
7 interfaces between chains.
- D–E · 947 Ų buried · 90 hydrogen bonds · nucleic-nucleic
- A–E · 417 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–E · 416 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–D · 411 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–D · 405 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 4ZQ9 · X-ray structure of AAV-2 OBD bound to AAVS1 site 3:1 · 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 P03132
- Elsewhere: RCSB PDB 4ZQ9 · PDBe 4ZQ9 · UniProt P03132
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