Research workbench
Staphylococcus epidermidis RP62A CRISPR short effector complex with self RNA target and ATP
Analyse Staphylococcus epidermidis RP62A CRISPR short effector complex with self RNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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