MolNFT v1 · #189037 · protein + RNA
Staphylococcus epidermidis RP62A CRISPR short effector complex with self RNA target and ATP
7V01 · CRISPR system cms endoribonuclease CSM3: “Staphylococcus epidermidis RP62A CRISPR short effector complex with self RNA target and ATP”. Electron microscopy, 1 ligand (ATP), 20 pockets (best druggability 0.88). MolNFT v1 #189037 on…
- PDB
- 7V01
- Type
- protein + RNA
- Length
- 2,183 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR system cms endoribonuclease CSM3; CRISPR system cms protein CSM5; CRISPR system…
- UniProt
- Q5HK91, Q5HK93, Q5HK89, Q5HK92, Q5HK90
- Ligands
- ATP
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 8 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | CRISPR system cms endoribonuclease CSM3 | protein | 205 | 27% helix, 28% strand | Q5HK91 |
| B | CRISPR system cms endoribonuclease CSM3 | protein | 192 | 27% helix, 30% strand | Q5HK91 |
| E | CRISPR system cms protein CSM5 | protein | 302 | 36% helix, 28% strand | Q5HK93 |
| F | CRISPR system single-strand-specific deoxyribonuclease CAS10/CSM1 (subtype III-a) | protein | 693 | 53% helix, 12% strand | Q5HK89 |
| G | RNA (37-mer) | rna | 30 | — | — |
| H | CRISPR system cms protein CSM4 | protein | 297 | 23% helix, 22% strand | Q5HK92 |
| I, K | CRISPR system cms protein CSM2 | protein | 117 | 75% helix, 5% strand | Q5HK90 |
| U | RNA (37-mer) | rna | 25 | — | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains F, 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 | 1036 | 0.88 | 0.90 | 125 | empty |
| 2 | 1115 | 0.82 | 0.83 | 116 | ATP |
| 3 | 406 | 0.80 | 0.89 | 43 | empty |
| 4 | 440 | 0.77 | 0.86 | 69 | empty |
| 5 | 337 | 0.77 | 0.88 | 37 | empty |
Interfaces
31 interfaces between chains.
- G–H · 1588 Ų buried · 31 hydrogen bonds · protein-nucleic
- F–H · 1488 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1457 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1412 Ų buried · 13 hydrogen bonds · protein-protein
- A–G · 1236 Ų buried · 38 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7V01 · Staphylococcus epidermidis RP62a CRISPR short effector complex with self RNA target and… · 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 Q5HK91
- Every structure of UniProt Q5HK93
- Every structure of UniProt Q5HK89
- Every structure of UniProt Q5HK92
- Every structure of UniProt Q5HK90
- Elsewhere: RCSB PDB 7V01 · PDBe 7V01 · UniProt Q5HK91 · UniProt Q5HK93 · UniProt Q5HK89 · UniProt Q5HK92 · UniProt Q5HK90
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.