MolNFT v1 · #179006 · protein + DNA
Adeno-associated virus origin binding domain in complex with ssdna
7JSE · Protein REP68: “Adeno-associated virus origin binding domain in complex with ssdna”. Electron microscopy, 20 pockets (best druggability 0.47). MolNFT v1 #179006 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7JSE
- Type
- protein + DNA
- Length
- 3,200 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein REP68; DNA (5'-D(*TP*TP*TP*T)-3')
- EC
- 3.6.4.12
- UniProt
- P03132
- Pockets
- 20 · best druggability 0.47
Structure
electron microscopy · 2 distinct chains · 32% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P | Protein REP68 (EC 3.6.4.12) | protein | 198 | 32% helix, 14% strand | P03132 |
| Q, R, S, T, U, V, W, X | DNA (5'-D(*TP*TP*TP*T)-3') | dna | 4 | — | — |
Pockets
20 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.47 | 0.72 | 51 | empty |
| 2 | 268 | 0.45 | 0.72 | 46 | empty |
| 3 | 242 | 0.43 | 0.72 | 43 | empty |
| 4 | 227 | 0.42 | 0.72 | 46 | empty |
| 5 | 220 | 0.42 | 0.72 | 46 | empty |
Interfaces
32 interfaces between chains.
- C–D · 121 Ų buried · 2 hydrogen bonds · protein-protein
- G–H · 119 Ų buried · 2 hydrogen bonds · protein-protein
- M–N · 119 Ų buried · 2 hydrogen bonds · protein-protein
- I–J · 118 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 117 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7JSE · 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 7JSE · PDBe 7JSE · UniProt P03132
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