MolNFT v1 · #134617 · protein + DNA
Crystal structure of human GEN1 in complex with holliday junction DNA in the upper interface
5T9J · Flap endonuclease gen homolog 1: “Crystal structure of human GEN1 in complex with holliday junction DNA in the upper interface”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.72). MolNFT v1 #134617 on GenesisL1…
- 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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