Research workbench
The structure of holo type human cu, zn superoxide dismutase
Analyse The structure of holo type human cu, zn superoxide dismutase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HL5
- Type
- protein
- Length
- 2,738 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase
- EC
- 1.15.1.1
- UniProt
- P00441
- Ligands
- CU, ZN, CA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, G, H, I, J, K, N, O, Q, S | Superoxide dismutase (EC 1.15.1.1) | protein | 153 | 6% helix, 41% strand | P00441 |
| E | Superoxide dismutase (EC 1.15.1.1) | protein | 151 | 6% helix, 42% strand | P00441 |
| F | Superoxide dismutase (EC 1.15.1.1) | protein | 144 | 6% helix, 39% strand | P00441 |
| L | Superoxide dismutase (EC 1.15.1.1) | protein | 152 | 6% helix, 40% strand | P00441 |
| M | Superoxide dismutase (EC 1.15.1.1) | protein | 150 | 5% helix, 40% strand | P00441 |
| P | Superoxide dismutase (EC 1.15.1.1) | protein | 152 | 6% helix, 41% strand | P00441 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 18 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, S
- ZN · Zinc ion · metal · 18 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, S
- CA · Calcium ion · metal · 3 copies · chains C, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.76 | 0.78 | 123 | empty |
| 2 | 873 | 0.75 | 0.79 | 91 | empty |
| 3 | 1074 | 0.74 | 0.77 | 109 | empty |
| 4 | 680 | 0.71 | 0.78 | 67 | empty |
| 5 | 708 | 0.71 | 0.78 | 95 | empty |
Interfaces
36 interfaces between chains.
- F–M · 722 Ų buried · 4 hydrogen bonds · protein-protein
- D–K · 721 Ų buried · 4 hydrogen bonds · protein-protein
- P–S · 719 Ų buried · 4 hydrogen bonds · protein-protein
- A–H · 719 Ų buried · 4 hydrogen bonds · protein-protein
- B–I · 716 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 1HL5 · The Structure of Holo 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 1HL5 · PDBe 1HL5 · UniProt P00441
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