MolNFT v2 · #155485 · protein
fused To-MtbCsm1 with 2ATP
6KC0 · CRISPR system single-strand-specific deoxyribonuclease…: “fused To-MtbCsm1 with 2ATP”. X-ray diffraction at 2.295, 2 ligands (ATP, MG), 9 pockets (best druggability 0.81). MolNFT v2 #155485 on GenesisL1: 3D structure, binding sites…
- PDB
- 6KC0
- Type
- protein
- Length
- 674 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.295
- Source
- Mycobacterium tuberculosis H37Rv; Thermococcus onnurineus NA1
- Molecule
- CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A),CRISPR…
- EC
- 3.1.-.-, 2.7.7.-
- UniProt
- B6YWB8, P71629
- Ligands
- ATP, MG
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.295 · 1 distinct chain · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A),CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A) (EC 3.1.-.-, 2.7.7.-) | protein | 674 | 51% helix, 15% strand | B6YWB8, P71629 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 697 | 0.81 | 0.85 | 71 | ATP, MG |
| 2 | 104 | 0.71 | 0.93 | 19 | empty |
| 3 | 158 | 0.48 | 0.77 | 22 | empty |
| 4 | 129 | 0.45 | 0.76 | 16 | empty |
| 5 | 98 | 0.44 | 0.78 | 20 | empty |
Modifications
Observed in the structure: 3 covalent, 3 disulfide (covalent ligand, disulfide).
Compared structures
- 6KC0 · Fused to-MTBCSM1 with 2ATP · the same entry in another collection · chain A against A, 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 0.96
- P71629 · AlphaFold monomer V2.0 prediction for CRISPR system single-strand- specific… · a predicted model of the same protein · chain A against A, TM-score 0.92
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 B6YWB8
- Every structure of UniProt P71629
- Elsewhere: RCSB PDB 6KC0 · PDBe 6KC0 · UniProt B6YWB8 · UniProt P71629
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