MolNFT v1 · #189038 · protein + RNA
Staphylococcus epidermidis RP62A CRISPR short effector complex
7V02 · CRISPR system cms endoribonuclease CSM3: “Staphylococcus epidermidis RP62A CRISPR short effector complex”. Electron microscopy, 20 pockets (best druggability 0.82). MolNFT v1 #189038 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7V02
- Type
- protein + RNA
- Length
- 2,099 residues
- Chains
- 9
- 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
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 7 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | CRISPR system cms endoribonuclease CSM3 | protein | 205 | 29% helix, 29% strand | Q5HK91 |
| B | CRISPR system cms endoribonuclease CSM3 | protein | 192 | 27% helix, 33% strand | Q5HK91 |
| E | CRISPR system cms protein CSM5 | protein | 288 | 36% helix, 26% strand | Q5HK93 |
| F | CRISPR system single-strand-specific deoxyribonuclease CAS10/CSM1 (subtype III-a) | protein | 650 | 54% helix, 13% strand | Q5HK89 |
| G | RNA (37-mer) | rna | 29 | — | — |
| H | CRISPR system cms protein CSM4 | protein | 296 | 19% helix, 20% strand | Q5HK92 |
| I, K | CRISPR system cms protein CSM2 | protein | 117 | 75% helix, 5% strand | Q5HK90 |
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 | 856 | 0.82 | 0.85 | 82 | empty |
| 2 | 808 | 0.81 | 0.84 | 73 | empty |
| 3 | 623 | 0.79 | 0.84 | 57 | empty |
| 4 | 747 | 0.78 | 0.82 | 70 | empty |
| 5 | 158 | 0.77 | 0.93 | 27 | empty |
Interfaces
24 interfaces between chains.
- G–H · 1616 Ų buried · 32 hydrogen bonds · protein-nucleic
- F–H · 1519 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1502 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1453 Ų buried · 12 hydrogen bonds · protein-protein
- B–H · 1223 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7V02 · Staphylococcus epidermidis RP62A CRISPR short effector complex · 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 7V02 · PDBe 7V02 · UniProt Q5HK91 · UniProt Q5HK93 · UniProt Q5HK89 · UniProt Q5HK92 · UniProt Q5HK90
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