MolNFT v1 · #38081 · protein + DNA
An activated, tetrameric gamma-delta resolvase: hin chimaera bound to cleaved DNA
2GM4 · 5'-D(*CP*AP*GP*TP*GP*TP*CP*CP*GP*AP*TP*AP*AP*TP*TP*TP*AP*TP…: “An activated, tetrameric gamma-delta resolvase: hin chimaera bound to cleaved DNA”. X-ray diffraction, 8 pockets (best druggability 0.60). MolNFT v1 #38081 on GenesisL1…
- PDB
- 2GM4
- Type
- protein + DNA
- Length
- 423 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*AP*GP*TP*GP*TP*CP*CP*GP*AP*TP*AP*AP*TP*TP*TP*AP*TP *AP*AP*A)-3'…
- UniProt
- P03012
- Pockets
- 8 · best druggability 0.60
Structure
x-ray diffraction · 7 distinct chains · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | 5'-D(*CP*AP*GP*TP*GP*TP*CP*CP*GP*AP*TP*AP*AP*TP*TP*TP*AP*TP *AP*AP*A)-3' | dna | 18 | — | — |
| Z, I | 5'-D(*CP*AP*GP*TP*GP*TP*CP*CP*GP*AP*TP*AP*AP*TP*TP*TP*AP*TP *AP*AP*A)-3' | dna | 3 | — | — |
| Y | 5'-D(*TP*TP*AP*TP*CP*GP*GP*AP*CP*AP*CP*TP*G)-3' | dna | 13 | — | — |
| J | 5'-D(*CP*AP*GP*TP*GP*TP*CP*CP*GP*AP*TP*AP*AP*TP*TP*TP*AP*TP *AP*AP*A)-3' | dna | 17 | — | — |
| K | 5'-D(*TP*TP*AP*TP*CP*GP*GP*AP*CP*AP*CP*TP*G)-3' | dna | 12 | — | — |
| A | Transposon gamma-delta resolvase | protein | 179 | 53% helix, 11% strand | P03012 |
| B | Transposon gamma-delta resolvase | protein | 178 | 50% helix, 12% strand | P03012 |
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.60 | 0.79 | 40 | empty |
| 2 | 81 | 0.49 | 0.83 | 16 | empty |
| 3 | 187 | 0.49 | 0.77 | 28 | empty |
| 4 | 100 | 0.34 | 0.74 | 14 | empty |
| 5 | 78 | 0.34 | 0.75 | 17 | empty |
Interfaces
13 interfaces between chains.
- J–B · 763 Ų buried · 2 hydrogen bonds · protein-nucleic
- X–A · 661 Ų buried · 3 hydrogen bonds · protein-nucleic
- A–B · 646 Ų buried · 1 hydrogen bond · protein-protein
- K–B · 589 Ų buried · 8 hydrogen bonds · protein-nucleic
- X–Y · 571 Ų buried · 54 hydrogen bonds · nucleic-nucleic
Compared structures
- 2GM4 · An activated, tetrameric gamma-delta resolvase: Hin chimaera bound to cleaved DNA · the same entry in another collection · chain B against B, TM-score 1.00
- P03012 · AlphaFold monomer V2.0 prediction for transposon gamma-delta resolvase (P03012) · a predicted model of the same protein · chain B against A, TM-score 0.87
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 2GM4 · PDBe 2GM4 · UniProt P03012
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