MolNFT v1 · #101677 · protein
The 1.8 ångström crystal structure of the periplasmic divalent cation tolerance protein cuta from pyrococcus horikoshii OT3
4NYO · Divalent-cation tolerance protein cuta: “The 1.8 ångström crystal structure of the periplasmic divalent cation tolerance protein cuta from pyrococcus…”. X-ray diffraction, 3 ligands (NA, CL, SO4), 7 pockets (best druggability 0.86).…
- 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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