Research workbench
The structure of PRIREP1 with dsdna
Analyse The structure of PRIREP1 with dsdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PDS
- Type
- protein + DNA
- Length
- 2,719 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Similar to D. nodosus vape; Polya
- UniProt
- Q8VLX1
- Ligands
- AGS, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 7 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Similar to D. nodosus vape | protein | 457 | 40% helix, 13% strand | Q8VLX1 |
| B | Similar to D. nodosus vape | protein | 448 | 40% helix, 15% strand | Q8VLX1 |
| C | Similar to D. nodosus vape | protein | 451 | 41% helix, 14% strand | Q8VLX1 |
| D | Similar to D. nodosus vape | protein | 454 | 41% helix, 15% strand | Q8VLX1 |
| E | Similar to D. nodosus vape | protein | 453 | 39% helix, 17% strand | Q8VLX1 |
| F | Similar to D. nodosus vape | protein | 451 | 37% helix, 13% strand | Q8VLX1 |
| M | Polya | dna | 5 | — | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.86 | 0.87 | 86 | empty |
| 2 | 1018 | 0.84 | 0.85 | 102 | empty |
| 3 | 1044 | 0.82 | 0.83 | 86 | AGS |
| 4 | 813 | 0.76 | 0.80 | 91 | empty |
| 5 | 680 | 0.75 | 0.81 | 84 | empty |
Interfaces
12 interfaces between chains.
- B–C · 2859 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2857 Ų buried · 54 hydrogen bonds · protein-protein
- D–E · 2811 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2805 Ų buried · 42 hydrogen bonds · protein-protein
- A–F · 2497 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 7PDS · The structure of PriRep1 with dsDNA · the same entry in another collection · chain F against F, 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 Q8VLX1
- Elsewhere: RCSB PDB 7PDS · PDBe 7PDS · UniProt Q8VLX1
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