Research workbench
Crystal structure of human apo CU,ZN superoxide dismutase (SOD1) complexed with cisplatin
Analyse Crystal structure of human apo CU,ZN superoxide dismutase (SOD1) complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RE0
- Type
- protein
- Length
- 555 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase [cu-zn]
- EC
- 1.15.1.1
- UniProt
- P00441
- Ligands
- CPT
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 153 | 7% helix, 39% strand | P00441 |
| C | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 126 | 4% helix, 48% strand | P00441 |
| D | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 123 | 7% helix, 49% strand | P00441 |
Ligands and binding sites
- CPT · Cisplatin · ligand · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.63 | 0.85 | 28 | empty |
| 2 | 208 | 0.63 | 0.83 | 36 | empty |
| 3 | 134 | 0.39 | 0.74 | 20 | CPT |
| 4 | 114 | 0.36 | 0.74 | 25 | empty |
| 5 | 104 | 0.33 | 0.72 | 20 | CPT |
Interfaces
4 interfaces between chains.
- A–B · 735 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 723 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 434 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 141 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3RE0 · Crystal structure of human apo Cu,Zn superoxide dismutase (SOD1) complexed with cisplatin · 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 P00441
- Elsewhere: RCSB PDB 3RE0 · PDBe 3RE0 · UniProt P00441
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