Research workbench
X-ray structure of a cu-zn superoxide dismutase from haemophilus ducreyi with haem bound at the dimer interface
Analyse X-ray structure of a cu-zn superoxide dismutase from haemophilus ducreyi with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z9N
- Type
- protein
- Length
- 620 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
- Q59452
- Ligands
- HEM, CU, ZN
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 155 | 7% helix, 38% strand | Q59452 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B, C, D
- CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.71 | 0.90 | 30 | empty |
| 2 | 155 | 0.70 | 0.89 | 33 | empty |
| 3 | 301 | 0.55 | 0.75 | 36 | empty |
| 4 | 70 | 0.37 | 0.77 | 13 | empty |
| 5 | 62 | 0.35 | 0.78 | 12 | empty |
Interfaces
3 interfaces between chains.
- C–D · 758 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 758 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 149 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1Z9N · X-Ray structure of a Cu-Zn superoxide dismutase from Haemophilus ducreyi with haem bound… · the same entry in another collection · chain A against A, TM-score 1.00
- Q59452 · AlphaFold monomer V2.0 prediction for superoxide dismutase [cu-zn] (Q59452) · a predicted model of the same protein · 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 Q59452
- Elsewhere: RCSB PDB 1Z9N · PDBe 1Z9N · UniProt Q59452
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