Research workbench
X-ray crystal structure of a CRISPR-associated CMR5 family protein from thermus thermophilus HB8
Analyse X-ray crystal structure of a CRISPR-associated CMR5 family protein from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZOP
- Type
- protein
- Length
- 662 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein TTHB164
- UniProt
- Q53W05
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.46
Structure
x-ray diffraction · 6 distinct chains · 83% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein TTHB164 | protein | 113 | 81% helix, 0% strand | Q53W05 |
| B | Putative uncharacterized protein TTHB164 | protein | 112 | 83% helix, 0% strand | Q53W05 |
| C | Putative uncharacterized protein TTHB164 | protein | 108 | 83% helix, 0% strand | Q53W05 |
| D | Putative uncharacterized protein TTHB164 | protein | 107 | 83% helix, 0% strand | Q53W05 |
| E | Putative uncharacterized protein TTHB164 | protein | 111 | 83% helix, 0% strand | Q53W05 |
| F | Putative uncharacterized protein TTHB164 | protein | 111 | 83% helix, 0% strand | Q53W05 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 192 | 0.46 | 0.75 | 27 | empty |
| 2 | 141 | 0.38 | 0.72 | 22 | empty |
| 3 | 91 | 0.34 | 0.74 | 21 | empty |
| 4 | 91 | 0.33 | 0.73 | 19 | empty |
| 5 | 62 | 0.27 | 0.73 | 18 | empty |
Interfaces
8 interfaces between chains.
- C–F · 343 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 301 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 287 Ų buried · 0 hydrogen bonds · protein-protein
- E–F · 276 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 275 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2ZOP · X-ray crystal structure of a CRISPR-associated Cmr5 family protein from Thermus… · the same entry in another collection · chain F against F, TM-score 1.00
- Q53W05 · AlphaFold monomer V2.0 prediction for CRISPR system cmr subunit CMR5 (Q53W05) · a predicted model of the same protein · chain F against A, TM-score 0.99
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 Q53W05
- Elsewhere: RCSB PDB 2ZOP · PDBe 2ZOP · UniProt Q53W05
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