MolNFT v1 · #104978 · protein + DNA
Crystal structure of T. fusca CAS3-amppnp
4QQZ · CRISPR-associated helicase, CAS3 family: “Crystal structure of T. fusca CAS3-amppnp”. X-ray diffraction, 2 ligands (ANP, FE), 20 pockets (best druggability 0.88). MolNFT v1 #104978 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4QQZ
- Type
- protein + DNA
- Length
- 3,632 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated helicase, CAS3 family; DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3…
- UniProt
- Q47PJ0
- Ligands
- ANP, FE
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated helicase, CAS3 family | protein | 903 | 44% helix, 14% strand | Q47PJ0 |
| B, D, F, H | DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') | dna | 9 | — | — |
| C | CRISPR-associated helicase, CAS3 family | protein | 902 | 44% helix, 14% strand | Q47PJ0 |
| E | CRISPR-associated helicase, CAS3 family | protein | 899 | 43% helix, 14% strand | Q47PJ0 |
| G | CRISPR-associated helicase, CAS3 family | protein | 892 | 43% helix, 13% strand | Q47PJ0 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, C, E, G
- FE · Fe (III) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1157 | 0.88 | 0.90 | 133 | empty |
| 2 | 864 | 0.87 | 0.89 | 92 | empty |
| 3 | 634 | 0.86 | 0.91 | 81 | empty |
| 4 | 804 | 0.86 | 0.89 | 95 | empty |
| 5 | 299 | 0.82 | 0.93 | 55 | empty |
Interfaces
12 interfaces between chains.
- A–C · 1800 Ų buried · 13 hydrogen bonds · protein-protein
- E–G · 1698 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1491 Ų buried · 34 hydrogen bonds · protein-nucleic
- G–H · 1484 Ų buried · 31 hydrogen bonds · protein-nucleic
- C–D · 1472 Ų buried · 31 hydrogen bonds · protein-nucleic
Compared structures
- 4QQZ · Crystal structure of T. fusca Cas3-AMPPNP · the same entry in another collection · chain A against A, 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 Q47PJ0
- Elsewhere: RCSB PDB 4QQZ · PDBe 4QQZ · UniProt Q47PJ0
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