MolNFT v1 · #141045 · protein
Native structure of HSOD1 in P6322 space group
5YUL · Superoxide dismutase [cu-zn]: “Native structure of HSOD1 in P6322 space group”. X-ray diffraction, 2 ligands (S4P, ZN), 13 pockets (best druggability 0.79). MolNFT v1 #141045 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5YUL
- Type
- protein
- Length
- 1,511 residues
- Chains
- 10
- 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
- S4P, ZN
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H, B, C, D, E, G, I | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 154 | 8% helix, 40% strand | P00441 |
| F | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 153 | 8% helix, 39% strand | P00441 |
| J | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 126 | 4% helix, 48% strand | P00441 |
Ligands and binding sites
- S4P · Dihydrogen tetrasulfide · ligand · 4 copies · chains A, H, B, C, D, E, I, J
- ZN · Zinc ion · metal · 9 copies · chains A, H, B, C, D, E, F, G, I
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 941 | 0.79 | 0.81 | 95 | S4P |
| 2 | 535 | 0.66 | 0.78 | 73 | empty |
| 3 | 163 | 0.66 | 0.87 | 29 | empty |
| 4 | 160 | 0.64 | 0.86 | 31 | empty |
| 5 | 198 | 0.63 | 0.84 | 35 | empty |
Interfaces
12 interfaces between chains.
- F–G · 746 Ų buried · 4 hydrogen bonds · protein-protein
- A–H · 736 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 729 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 729 Ų buried · 4 hydrogen bonds · protein-protein
- I–J · 708 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 covalent (disulfide, covalent ligand).
Compared structures
- 5YUL · Native Structure of hSOD1 in P6322 space group · 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 5YUL · PDBe 5YUL · UniProt P00441
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