MolNFT v1 · #17796 · protein + DNA
Flpe W330F mutant-DNA holliday junction complex
1P4E · 5'-D(*TP*AP*AP*GP*TP*TP*CP*CP*TP*AP*TP*TP*C)-3': “Flpe W330F mutant-DNA holliday junction complex”. X-ray diffraction, 1 ligand (2PO), 20 pockets (best druggability 0.81). MolNFT v1 #17796 on GenesisL1: 3D structure, binding sites…
- PDB
- 1P4E
- Type
- protein + DNA
- Length
- 1,750 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*AP*AP*GP*TP*TP*CP*CP*TP*AP*TP*TP*C)-3'…
- UniProt
- P03870
- Ligands
- 2PO
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F | 5'-D(*TP*AP*AP*GP*TP*TP*CP*CP*TP*AP*TP*TP*C)-3' | dna | 13 | — | — |
| I, J | 5'-D(*TP*TP*TP*AP*AP*AP*AP*GP*AP*AP*TP*AP*GP*GP*AP*AP*CP*TP *TP*C)-3' | dna | 19 | — | — |
| G, H | 33-mer | dna | 32 | — | — |
| A | Recombinase flp protein | protein | 400 | 50% helix, 12% strand | P03870 |
| B | Recombinase flp protein | protein | 413 | 49% helix, 12% strand | P03870 |
| C | Recombinase flp protein | protein | 400 | 52% helix, 13% strand | P03870 |
| D | Recombinase flp protein | protein | 409 | 50% helix, 12% strand | P03870 |
Ligands and binding sites
- 2PO · Phosphonate · ligand · chains H, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1160 | 0.81 | 0.82 | 133 | empty |
| 2 | 356 | 0.78 | 0.88 | 51 | empty |
| 3 | 367 | 0.77 | 0.87 | 54 | empty |
| 4 | 277 | 0.77 | 0.90 | 35 | empty |
| 5 | 553 | 0.73 | 0.81 | 64 | empty |
Interfaces
27 interfaces between chains.
- A–D · 1784 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1761 Ų buried · 22 hydrogen bonds · protein-protein
- H–D · 1179 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–D · 1117 Ų buried · 9 hydrogen bonds · protein-protein
- G–B · 1091 Ų buried · 28 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified, 1 covalent (phosphorylation, covalent ligand).
Compared structures
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 P03870
- Elsewhere: RCSB PDB 1P4E · PDBe 1P4E · UniProt P03870
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