Research workbench
The 1.8 ångström crystal structure of the periplasmic divalent cation tolerance protein cuta from pyrococcus horikoshii OT3
Analyse The 1.8 ångström crystal structure of the periplasmic divalent cation tolerance… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NYO
- Type
- protein
- Length
- 612 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Divalent-cation tolerance protein cuta
- UniProt
- O58720
- Ligands
- NA, CL, SO4
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Divalent-cation tolerance protein cuta | protein | 102 | 36% helix, 37% strand | O58720 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 2 copies · chains C, D, E, F
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, B, C, D, E, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.86 | 0.98 | 20 | SO4 |
| 2 | 185 | 0.85 | 0.98 | 17 | CL |
| 3 | 950 | 0.82 | 0.83 | 113 | SO4 |
| 4 | 90 | 0.59 | 0.87 | 15 | MES |
| 5 | 90 | 0.57 | 0.86 | 15 | MES |
Interfaces
13 interfaces between chains.
- A–B · 1174 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1152 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 1150 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1129 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1100 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (oxidation).
Compared structures
- 4NYO · The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein… · the same entry in another collection · chain F against F, TM-score 1.00
- O58720 · AlphaFold monomer V2.0 prediction for divalent-cation tolerance protein cuta (O58720) · a predicted model of the same protein · chain B 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 O58720
- Elsewhere: RCSB PDB 4NYO · PDBe 4NYO · UniProt O58720
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