MolNFT v1 · #7678 · protein + DNA
Crystal structure of a site-specific recombinase, gamma- delta resolvase complexed with a 34 bp cleavage site
1GDT · Site I of res DNA: “Crystal structure of a site-specific recombinase, gamma- delta resolvase complexed with a 34 bp cleavage site”. X-ray diffraction, 5 pockets (best druggability 0.69). MolNFT v1 #7678 on GenesisL1: 3D structure…
- PDB
- 1GDT
- Type
- protein + DNA
- Length
- 435 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Site I of res DNA; Protein (gamma delta resolvase)
- UniProt
- P03012
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Site I of res DNA | dna | 22 | — | — |
| D, F | Site I of res DNA | dna | 13 | — | — |
| E | Site I of res DNA | dna | 21 | — | — |
| A, B | Protein (gamma delta resolvase) | protein | 183 | 56% helix, 11% strand | P03012 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 336 | 0.69 | 0.83 | 37 | empty |
| 2 | 198 | 0.51 | 0.77 | 29 | empty |
| 3 | 68 | 0.35 | 0.77 | 13 | empty |
| 4 | 57 | 0.34 | 0.78 | 12 | empty |
| 5 | 73 | 0.27 | 0.72 | 12 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1121 Ų buried · 9 hydrogen bonds · protein-protein
- C–A · 816 Ų buried · 12 hydrogen bonds · protein-nucleic
- E–B · 805 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–F · 644 Ų buried · 53 hydrogen bonds · nucleic-nucleic
- D–E · 596 Ų buried · 53 hydrogen bonds · nucleic-nucleic
Compared structures
- 1GDT · Crystal structure of a site-specific recombinase, gamma-delta resolvase complexed with a… · the same entry in another collection · chain E against E, TM-score 1.00
- P03012 · AlphaFold monomer V2.0 prediction for transposon gamma-delta resolvase (P03012) · a predicted model of the same protein · chain A against A, TM-score 0.61
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 P03012
- Elsewhere: RCSB PDB 1GDT · PDBe 1GDT · UniProt P03012
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