MolNFT v1 · #105554 · protein + DNA
Crystal structure of PAFAN1 - 5' flap DNA complex with manganase
4R89 · Uncharacterized protein: “Crystal structure of PAFAN1 - 5' flap DNA complex with manganase”. X-ray diffraction, 1 ligand (MN), 20 pockets (best druggability 0.82). MolNFT v1 #105554 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4R89
- Type
- protein + DNA
- Length
- 1,168 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein; DNA (5'-D(P*AP*CP*CP*AP*GP*AP*CP*AP*CP*AP*CP*AP*TP*TP*C)- 3')…
- UniProt
- Q9I2N0
- Ligands
- MN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Uncharacterized protein | protein | 537 | 51% helix, 7% strand | Q9I2N0 |
| B, F | DNA (5'-D(P*AP*CP*CP*AP*GP*AP*CP*AP*CP*AP*CP*AP*TP*TP*C)- 3') | dna | 15 | — | — |
| C, G | DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3') | dna | 10 | — | — |
| D, H | 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*C) -3') | dna | 22 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1172 | 0.82 | 0.84 | 95 | empty |
| 2 | 544 | 0.79 | 0.86 | 56 | empty |
| 3 | 135 | 0.65 | 0.87 | 32 | empty |
| 4 | 554 | 0.64 | 0.76 | 33 | empty |
| 5 | 189 | 0.63 | 0.84 | 33 | empty |
Interfaces
12 interfaces between chains.
- A–B · 954 Ų buried · 16 hydrogen bonds · protein-nucleic
- E–F · 944 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–D · 813 Ų buried · 17 hydrogen bonds · protein-nucleic
- E–H · 809 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–E · 666 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4R89 · Crystal structure of paFAN1 - 5' flap DNA complex with Manganase · the same entry in another collection · chain H against H, 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 E 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 Q9I2N0
- Elsewhere: RCSB PDB 4R89 · PDBe 4R89 · UniProt Q9I2N0
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