Research workbench
Crystal structure of human GEN1 in complex with holliday junction DNA in the upper interface
Analyse Crystal structure of human GEN1 in complex with holliday junction DNA in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T9J
- Type
- protein + DNA
- Length
- 859 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flap endonuclease gen homolog 1; DNA (5'- D(*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DGP*DGP*DAP*DTP*D…
- EC
- 3.1.-.-
- UniProt
- Q17RS7
- Ligands
- MG
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Flap endonuclease gen homolog 1 (EC 3.1.-.-) | protein | 390 | 47% helix, 15% strand | Q17RS7 |
| B | Flap endonuclease gen homolog 1 (EC 3.1.-.-) | protein | 391 | 48% helix, 15% strand | Q17RS7 |
| C | DNA (5'- D(*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DAP*DGP*DGP*DGP*DA P*DTP*DGP*DC)-3') | dna | 20 | — | — |
| D | DNA (5'- D(*DGP*DCP*DAP*DTP*DCP*DCP*DCP*DTP*DAP*DAP*DGP*DCP*DTP*DCP*DCP*DAP*DT P*DCP*DGP*DT)-3') | dna | 20 | — | — |
| E | DNA (5'- D(*DAP*DCP*DGP*DAP*DTP*DGP*DGP*DAP*DGP*DCP*DCP*DGP*DCP*DTP*DAP*DGP*DG P*DCP*DTP*DC)-3') | dna | 19 | — | — |
| F | DNA (5'- D(*DGP*DAP*DGP*DCP*DCP*DTP*DAP*DGP*DCP*DGP*DTP*DCP*DCP*DGP*DGP*DAP*DA P*DTP*DTP*DC)-3') | dna | 19 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 15 copies · chains A, C, B, E, F, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1047 | 0.72 | 0.76 | 55 | GOL |
| 2 | 1068 | 0.72 | 0.76 | 63 | empty |
| 3 | 126 | 0.71 | 0.91 | 18 | GOL |
| 4 | 119 | 0.70 | 0.91 | 18 | empty |
| 5 | 98 | 0.65 | 0.90 | 20 | empty |
Interfaces
10 interfaces between chains.
- A–C · 546 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–F · 508 Ų buried · 38 hydrogen bonds · nucleic-nucleic
- A–D · 471 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–E · 459 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–D · 457 Ų buried · 49 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 5T9J · Crystal Structure of human GEN1 in complex with Holliday junction DNA in the upper… · the same entry in another collection · chain F against F, TM-score 1.00
- Q17RS7 · AlphaFold monomer V2.0 prediction for flap endonuclease gen homolog 1 (Q17RS7) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q17RS7
- Elsewhere: RCSB PDB 5T9J · PDBe 5T9J · UniProt Q17RS7
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