MolNFT v1 · #69138 · protein
Crystal structure of human CU/ZN superoxide dismutase recombinantly produced in leishmania tarantolae; P6522 crystal form containing 6 chains in the asymmetric unit
3KH4 · Superoxide dismutase [cu-zn]: “Crystal structure of human CU/ZN superoxide dismutase recombinantly produced in leishmania tarantolae; P6522…”. X-ray diffraction, 2 ligands (CU, ZN), 8 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 3KH4
- Type
- protein
- Length
- 918 residues
- Chains
- 6
- 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
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 153 | 7% helix, 41% strand | P00441 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 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
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.76 | 0.79 | 100 | empty |
| 2 | 222 | 0.60 | 0.81 | 27 | empty |
| 3 | 238 | 0.59 | 0.80 | 32 | empty |
| 4 | 224 | 0.59 | 0.80 | 26 | empty |
| 5 | 191 | 0.53 | 0.78 | 27 | empty |
Interfaces
6 interfaces between chains.
- C–D · 691 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 680 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 677 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 391 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 356 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3KH4 · 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 3KH4 · PDBe 3KH4 · UniProt P00441
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