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The 2.0 ångström crystal structure of pyrococcus horikoshii CUTA1 complexed with na+
Analyse The 2.0 ångström crystal structure of pyrococcus horikoshii CUTA1 complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NYP
- 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, SO4
- Pockets
- 9 · best druggability 0.87
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 · 3 copies · chains A, C, E, F, B, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.87 | 0.98 | 19 | SO4 |
| 2 | 198 | 0.85 | 0.98 | 21 | SO4 |
| 3 | 409 | 0.76 | 0.85 | 55 | empty |
| 4 | 436 | 0.73 | 0.83 | 62 | SO4 |
| 5 | 108 | 0.60 | 0.86 | 16 | SO4 |
Interfaces
13 interfaces between chains.
- B–C · 1155 Ų buried · 22 hydrogen bonds · protein-protein
- D–F · 1151 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1146 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1130 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1123 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (oxidation).
Compared structures
- 4NYP · The 2.0 Angstrom Crystal Structure of Pyrococcus Horikoshii Cuta1 Complexed With NA+ · 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 E against A, TM-score 1.00
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 4NYP · PDBe 4NYP · UniProt O58720
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