MolNFT v1 · #158871 · protein
Crystal structure of CSM1-CSM4 cassette in complex with amppnp
6O74: “Crystal structure of CSM1-CSM4 cassette in complex with amppnp”. X-ray diffraction, 2 ligands (ANP, MN), 14 pockets (best druggability 0.83). MolNFT v1 #158871 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6O74
- Type
- protein
- Length
- 954 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CSM4; CSM1
- EC
- 3.1.-.-, 2.7.7.-
- UniProt
- B6YWC1, B6YWB8
- Ligands
- ANP, MN
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | CSM4 | protein | 250 | 26% helix, 35% strand | B6YWC1 |
| A | CSM1 (EC 3.1.-.-, 2.7.7.-) | protein | 704 | 47% helix, 15% strand | B6YWB8 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains B, A
- MN · Manganese (II) ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1120 | 0.83 | 0.84 | 96 | ANP, MN |
| 2 | 472 | 0.70 | 0.80 | 50 | empty |
| 3 | 97 | 0.50 | 0.82 | 21 | empty |
| 4 | 139 | 0.49 | 0.78 | 22 | empty |
| 5 | 101 | 0.42 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- B–A · 1421 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6O74 · Crystal structure of Csm1-Csm4 cassette in complex with AMPPNP · the same entry in another collection · chain B against B, TM-score 1.00
- B6YWB8 · AlphaFold monomer V2.0 prediction for CRISPR system single-strand- specific… · a predicted model of the same protein · chain A against A, TM-score 0.99
- B6YWC1 · AlphaFold monomer V2.0 prediction for CRISPR system cms protein CSM4 (B6YWC1) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 B6YWC1
- Every structure of UniProt B6YWB8
- Elsewhere: RCSB PDB 6O74 · PDBe 6O74 · UniProt B6YWC1 · UniProt B6YWB8
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