Research workbench
Crystal structure of PAFAN1 bound to 1NT 5'FLAP DNA with gap
Analyse Crystal structure of PAFAN1 bound to 1NT 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
- 5Y7G
- Type
- protein + DNA
- Length
- 1,768 residues
- Chains
- 12
- 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
- CA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 7 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fanconi-associated nuclease 1 homolog (EC 3.1.4.1) | protein | 542 | 51% helix, 9% strand | Q9I2N0 |
| B | Fanconi-associated nuclease 1 homolog (EC 3.1.4.1) | protein | 543 | 53% helix, 9% strand | Q9I2N0 |
| C | Fanconi-associated nuclease 1 homolog (EC 3.1.4.1) | protein | 540 | 51% helix, 9% strand | Q9I2N0 |
| D, F, H | DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3') | dna | 10 | — | — |
| E, G, I | 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 | 24 | — | — |
| J, L | DNA (5'-D(P*TP*GP*AP*CP*AP*CP*AP*CP*AP*TP*TP*CP*AP*A)-3') | dna | 14 | — | — |
| N | DNA (5'-D(P*TP*GP*AP*CP*AP*CP*AP*CP*AP*TP*TP*CP*AP*A)-3') | dna | 13 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains A, J, B, L, C, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.78 | 0.92 | 26 | empty |
| 2 | 704 | 0.78 | 0.83 | 64 | empty |
| 3 | 828 | 0.76 | 0.81 | 56 | empty |
| 4 | 870 | 0.76 | 0.80 | 63 | empty |
| 5 | 792 | 0.76 | 0.80 | 52 | empty |
Interfaces
18 interfaces between chains.
- B–G · 860 Ų buried · 19 hydrogen bonds · protein-nucleic
- C–I · 804 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–E · 710 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–J · 622 Ų buried · 17 hydrogen bonds · protein-nucleic
- C–N · 552 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 5Y7G · Crystal structure of paFAN1 bound to 1nt 5'flap DNA with gap · the same entry in another collection · chain N against N, TM-score 1.00
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 5Y7G · PDBe 5Y7G · UniProt Q9I2N0
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