Research workbench
Crystal structure of human CU/ZN superoxide dismutase recombinantly produced in leishmania tarantolae; P212121 crystal form containing 12 chains in the asymmetric unit
Analyse Crystal structure of human CU/ZN superoxide dismutase recombinantly produced in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KH3
- Type
- protein
- Length
- 1,836 residues
- Chains
- 12
- 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
- CU, ZN, SO4
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 153 | 4% helix, 41% strand | P00441 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- SO4 · Sulfate ion · ion · 3 copies · chains B, C, F, H, J, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 560 | 0.71 | 0.80 | 66 | SO4 |
| 2 | 1056 | 0.70 | 0.74 | 85 | empty |
| 3 | 538 | 0.69 | 0.79 | 61 | SO4 |
| 4 | 630 | 0.65 | 0.75 | 55 | empty |
| 5 | 613 | 0.65 | 0.75 | 60 | empty |
Interfaces
17 interfaces between chains.
- C–D · 701 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 698 Ų buried · 4 hydrogen bonds · protein-protein
- I–J · 697 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 690 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 690 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3KH3 · Crystal structure of human Cu/Zn superoxide dismutase recombinantly produced in… · 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 3KH3 · PDBe 3KH3 · UniProt P00441
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