MolNFT v1 · #138766 · protein + DNA + RNA
Crystal structure of the CRISPR-associated protein in complex with crrna and DNA
5WTI · DNA (28-mer): “Crystal structure of the CRISPR-associated protein in complex with crrna and DNA”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.83). MolNFT v1 #138766 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5WTI
- Type
- protein + DNA + RNA
- Length
- 1,136 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (28-mer); DNA (5'-D(P*GP*TP*GP*TP*GP*GP*AP*TP*TP*CP*CP*G)-3'); CRISPR-associated…
- UniProt
- A0A0D0F5I0
- Ligands
- MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | DNA (28-mer) | dna | 28 | — | — |
| H | DNA (5'-D(P*GP*TP*GP*TP*GP*GP*AP*TP*TP*CP*CP*G)-3') | dna | 11 | — | — |
| Z | CRISPR-associated protein | protein | 982 | 45% helix, 16% strand | A0A0D0F5I0 |
| B | RNA (123-mer) | rna | 115 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 26 copies · chains H, Z, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.83 | 0.84 | 60 | MG |
| 2 | 154 | 0.80 | 0.96 | 25 | empty |
| 3 | 931 | 0.77 | 0.80 | 80 | MG |
| 4 | 320 | 0.77 | 0.89 | 41 | MG |
| 5 | 286 | 0.76 | 0.89 | 33 | MG |
Interfaces
5 interfaces between chains.
- Z–B · 6032 Ų buried · 147 hydrogen bonds · protein-nucleic
- E–Z · 2481 Ų buried · 57 hydrogen bonds · protein-nucleic
- H–Z · 1014 Ų buried · 16 hydrogen bonds · protein-nucleic
- E–B · 874 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- E–H · 413 Ų buried · 38 hydrogen bonds · nucleic-nucleic
Compared structures
- 5WTI · Crystal structure of the CRISPR-associated protein in complex with crRNA and DNA · the same entry in another collection · chain E against E, 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 A0A0D0F5I0
- Elsewhere: RCSB PDB 5WTI · PDBe 5WTI · UniProt A0A0D0F5I0
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