Research workbench
Crystal structure of PAFAN1 bound to 2NT 5'FLAP DNA with gap
Analyse Crystal structure of PAFAN1 bound to 2NT 5'FLAP DNA with gap in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y7Q
- Type
- protein + DNA
- Length
- 582 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fanconi-associated nuclease 1 homolog; DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3'); DNA…
- EC
- 3.1.4.1
- UniProt
- Q9I2N0
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fanconi-associated nuclease 1 homolog (EC 3.1.4.1) | protein | 546 | 53% helix, 10% strand | Q9I2N0 |
| D | DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3') | dna | 10 | — | — |
| B | DNA (5'-D(*TP*TP*CP*AP*CP*AP*CP*AP*TP*TP*CP*AP*A)-3') | dna | 7 | — | — |
| C | DNA (5'- D(P*GP*AP*AP*TP*GP*TP*GP*TP*GP*TP*CP*TP*CP*AP*AP*TP*CP*CP*CP*AP*AP*CP *TP*T)-3') | dna | 19 | — | — |
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 887 | 0.71 | 0.77 | 63 | empty |
| 2 | 341 | 0.65 | 0.80 | 35 | empty |
| 3 | 574 | 0.63 | 0.75 | 61 | empty |
| 4 | 465 | 0.61 | 0.76 | 33 | empty |
| 5 | 63 | 0.29 | 0.75 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–C · 916 Ų buried · 21 hydrogen bonds · protein-nucleic
- D–C · 456 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- A–D · 412 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 260 Ų buried · 19 hydrogen bonds · nucleic-nucleic
- A–B · 186 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 5Y7Q · Crystal structure of paFAN1 bound to 2nt 5'flap DNA with gap · the same entry in another collection · chain A against A, TM-score 1.00
- Q9I2N0 · AlphaFold monomer V2.0 prediction for fanconi-associated nuclease 1 homolog (Q9I2N0) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9I2N0
- Elsewhere: RCSB PDB 5Y7Q · PDBe 5Y7Q · UniProt Q9I2N0
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