MolNFT v1 · #9098 · protein
The structure of apo type human cu, zn superoxide dismutase
1HL4: “The structure of apo type human cu, zn superoxide dismutase”. X-ray diffraction, 2 ligands (ACE, ZN), 5 pockets (best druggability 0.63). MolNFT v1 #9098 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1HL4
- Type
- protein
- Length
- 558 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase
- EC
- 1.15.1.1
- UniProt
- P00441
- Ligands
- ACE, ZN
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Superoxide dismutase (EC 1.15.1.1) | protein | 153 | 5% helix, 41% strand | P00441 |
| C | Superoxide dismutase (EC 1.15.1.1) | protein | 127 | 6% helix, 48% strand | P00441 |
| D | Superoxide dismutase (EC 1.15.1.1) | protein | 125 | 4% helix, 49% strand | P00441 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.63 | 0.83 | 32 | empty |
| 2 | 196 | 0.60 | 0.82 | 29 | empty |
| 3 | 274 | 0.49 | 0.74 | 35 | empty |
| 4 | 158 | 0.40 | 0.73 | 26 | empty |
| 5 | 139 | 0.39 | 0.73 | 20 | empty |
Interfaces
4 interfaces between chains.
- C–D · 717 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 712 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 444 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 183 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 1HL4 · The Structure of Apo Type Human Cu, Zn Superoxide Dismutase · 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 1HL4 · PDBe 1HL4 · UniProt P00441
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