Research workbench
Structural basis for the recognition of attp substrates by P4-like integrases
Analyse Structural basis for the recognition of attp substrates by P4-like integrases in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RMP
- Type
- protein + DNA
- Length
- 207 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CP4-like integrase; 5'-D(*TP*AP*AP*TP*GP*AP*CP*CP*AP*CP*CP*AP*AP*TP*A)-3'…
- UniProt
- Q9Z3B4
- Pockets
- 5 · best druggability 0.53
Structure
x-ray diffraction · 5 distinct chains · 26% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CP4-like integrase | protein | 77 | 26% helix, 35% strand | Q9Z3B4 |
| C | CP4-like integrase | protein | 75 | 27% helix, 36% strand | Q9Z3B4 |
| E | 5'-D(*TP*AP*AP*TP*GP*AP*CP*CP*AP*CP*CP*AP*AP*TP*A)-3' | dna | 14 | — | — |
| F, H | 5'-D(*TP*AP*TP*TP*GP*GP*TP*GP*GP*TP*CP*AP*TP*TP*A)-3' | dna | 13 | — | — |
| G | 5'-D(*TP*AP*AP*TP*GP*AP*CP*CP*AP*CP*CP*AP*AP*TP*A)-3' | dna | 15 | — | — |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.53 | 0.81 | 29 | empty |
| 2 | 65 | 0.42 | 0.81 | 11 | empty |
| 3 | 104 | 0.42 | 0.78 | 16 | empty |
| 4 | 71 | 0.41 | 0.80 | 12 | empty |
| 5 | 52 | 0.26 | 0.74 | 12 | empty |
Interfaces
9 interfaces between chains.
- A–C · 640 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 603 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- E–F · 578 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- A–G · 566 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–E · 527 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 3RMP · Structural basis for the recognition of attP substrates by P4-like integrases · 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 Q9Z3B4
- Elsewhere: RCSB PDB 3RMP · PDBe 3RMP · UniProt Q9Z3B4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.