MolNFT v1 · #141420 · protein + DNA
Crystal structure of PAFAN1 bound to 2NT 5'FLAP DNA with gap with manganese
5Z6W · Fanconi-associated nuclease 1 homolog: “Crystal structure of PAFAN1 bound to 2NT 5'FLAP DNA with gap with manganese”. X-ray diffraction, 1 ligand (MN), 4 pockets (best druggability 0.75). MolNFT v1 #141420 on GenesisL1: 3D…
- 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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