MolNFT v1 · #119439 · protein + DNA + RNA
Crystal structure of SPCAS9 variant vrer bound to sgrna and tgcg pam target DNA
5FW3: “Crystal structure of SPCAS9 variant vrer bound to sgrna and tgcg pam target DNA”. X-ray diffraction, 2 ligands (K, MG), 20 pockets (best druggability 0.81). MolNFT v1 #119439 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5FW3
- Type
- protein + DNA + RNA
- Length
- 1,442 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sgrna; CRISPR-associated endonuclease CAS9/CSN1; Target DNA strand; Non-target DNA strand
- EC
- 3.1.-.-
- UniProt
- Q99ZW2
- Ligands
- K, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sgrna | rna | 81 | — | — |
| B | CRISPR-associated endonuclease CAS9/CSN1 (EC 3.1.-.-) | protein | 1322 | 49% helix, 12% strand | Q99ZW2 |
| C | Target DNA strand | dna | 28 | — | — |
| D | Non-target DNA strand | dna | 11 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.81 | 0.83 | 71 | K |
| 2 | 1157 | 0.78 | 0.80 | 86 | K |
| 3 | 439 | 0.76 | 0.86 | 38 | MG, K |
| 4 | 975 | 0.75 | 0.78 | 68 | empty |
| 5 | 85 | 0.68 | 0.93 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–B · 6061 Ų buried · 138 hydrogen bonds · protein-nucleic
- B–C · 1696 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–C · 965 Ų buried · 71 hydrogen bonds · nucleic-nucleic
- B–D · 660 Ų buried · 15 hydrogen bonds · protein-nucleic
- C–D · 401 Ų buried · 26 hydrogen bonds · nucleic-nucleic
Compared structures
- 5FW3 · Crystal structure of SpCas9 variant VRER bound to sgRNA and TGCG PAM target DNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q99ZW2 · AlphaFold monomer V2.0 prediction for CRISPR-associated endonuclease CAS9/CSN1 (Q99ZW2) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q99ZW2
- Elsewhere: RCSB PDB 5FW3 · PDBe 5FW3 · UniProt Q99ZW2
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