Research workbench
Novel purple cupredoxin from nitrosopumilus maritimus
Analyse Novel purple cupredoxin from nitrosopumilus maritimus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FC9
- Type
- protein
- Length
- 380 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Blue (type 1) copper domain protein
- UniProt
- A9A2G4
- Ligands
- CU
- Pockets
- 3 · best druggability 0.38
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Blue (type 1) copper domain protein | protein | 95 | 0% helix, 47% strand | A9A2G4 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.38 | 0.75 | 26 | empty |
| 2 | 98 | 0.37 | 0.75 | 25 | empty |
| 3 | 53 | 0.30 | 0.76 | 12 | empty |
Interfaces
5 interfaces between chains.
- A–D · 780 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 772 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 269 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 268 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 189 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5FC9 · Novel Purple Cupredoxin from Nitrosopumilus maritimus · the same entry in another collection · chain A 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 A9A2G4
- Elsewhere: RCSB PDB 5FC9 · PDBe 5FC9 · UniProt A9A2G4
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