Research workbench
Crystal structure of PAFAN1 bound to 2NT 5'FLAP DNA with gap with manganese
Analyse Crystal structure of PAFAN1 bound to 2NT 5'FLAP DNA with gap with manganese in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z6W
- Type
- protein + DNA
- Length
- 584 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
- Ligands
- MN
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fanconi-associated nuclease 1 homolog (EC 3.1.4.1) | protein | 546 | 50% helix, 8% strand | Q9I2N0 |
| H | DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3') | dna | 10 | — | — |
| B | DNA (5'-D(P*AP*TP*TP*CP*AP*A)-3') | dna | 6 | — | — |
| C | DNA (5'- D(P*GP*AP*AP*TP*GP*TP*GP*TP*CP*TP*CP*AP*AP*TP*CP*CP*CP*AP*AP*CP*TP*T) -3') | dna | 22 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 610 | 0.75 | 0.82 | 60 | empty |
| 2 | 672 | 0.74 | 0.80 | 54 | MN |
| 3 | 305 | 0.63 | 0.79 | 34 | empty |
| 4 | 501 | 0.62 | 0.76 | 33 | empty |
Interfaces
5 interfaces between chains.
- A–C · 935 Ų buried · 17 hydrogen bonds · protein-nucleic
- H–C · 455 Ų buried · 33 hydrogen bonds · nucleic-nucleic
- A–H · 413 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 259 Ų buried · 14 hydrogen bonds · nucleic-nucleic
- A–B · 151 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 5Z6W · Crystal structure of paFAN1 bound to 2nt 5'flap DNA with gap with Manganese · 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 5Z6W · PDBe 5Z6W · UniProt Q9I2N0
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