Research workbench
Crystal structure of CRISPR-associated protein in complex with 2'- deoxyadenosine 5'-triphosphate
Analyse Crystal structure of CRISPR-associated protein in complex with 2'… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q2D
- Type
- protein
- Length
- 927 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated helicase CAS3
- UniProt
- D1CGD0
- Ligands
- DTP, NI, MG
- Pockets
- 7 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated helicase CAS3 | protein | 927 | 45% helix, 13% strand | D1CGD0 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A
- NI · Nickel (II) ion · metal · 3 copies · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1166 | 0.87 | 0.88 | 103 | empty |
| 2 | 402 | 0.69 | 0.81 | 56 | MG, DTP |
| 3 | 180 | 0.50 | 0.77 | 35 | empty |
| 4 | 104 | 0.46 | 0.79 | 17 | empty |
| 5 | 100 | 0.44 | 0.78 | 26 | empty |
Modifications
Observed in the structure: 19 modified (engineered).
Compared structures
- 4Q2D · Crystal Structure of CRISPR-Associated protein in complex with 2'-Deoxyadenosine… · 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 D1CGD0
- Elsewhere: RCSB PDB 4Q2D · PDBe 4Q2D · UniProt D1CGD0
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