MolNFT v1 · #189036 · protein + RNA
Staphylococcus epidermidis RP62A CRISPR tall effector complex with bound ATP
7V00 · CRISPR system cms endoribonuclease CSM3: “Staphylococcus epidermidis RP62A CRISPR tall effector complex with bound ATP”. Electron microscopy, 1 ligand (ATP), 20 pockets (best druggability 0.83). MolNFT v1 #189036 on GenesisL1: 3D…
- PDB
- 7V00
- Type
- protein + RNA
- Length
- 2,460 residues
- Chains
- 11
- 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 0.83
Structure
electron microscopy · 9 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 |
| D | CRISPR system cms endoribonuclease CSM3 | protein | 199 | 27% helix, 30% strand | Q5HK91 |
| E | CRISPR system cms protein CSM5 | protein | 302 | 38% helix, 25% strand | Q5HK93 |
| F | CRISPR system single-strand-specific deoxyribonuclease CAS10/CSM1 (subtype III-a) | protein | 695 | 51% helix, 13% strand | Q5HK89 |
| G | RNA (37-mer) | rna | 30 | — | — |
| 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 |
| J | CRISPR system cms protein CSM2 | protein | 102 | 77% helix, 4% strand | Q5HK90 |
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 | 680 | 0.83 | 0.88 | 83 | empty |
| 2 | 833 | 0.82 | 0.84 | 102 | ATP |
| 3 | 1165 | 0.80 | 0.82 | 92 | empty |
| 4 | 664 | 0.80 | 0.84 | 57 | empty |
| 5 | 149 | 0.75 | 0.93 | 23 | empty |
Interfaces
32 interfaces between chains.
- G–H · 1601 Ų buried · 27 hydrogen bonds · protein-nucleic
- F–H · 1497 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1403 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1390 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1389 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7V00 · Staphylococcus epidermidis RP62a CRISPR tall effector complex with bound ATP · 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 7V00 · PDBe 7V00 · UniProt Q5HK91 · UniProt Q5HK93 · UniProt Q5HK89 · UniProt Q5HK92 · UniProt Q5HK90
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