MolNFT v1 · #86654 · protein
Monomeric human CU,ZN superoxide dismutase, loops IV and VII deleted, apo form, mutant H43F
4BD4 · Superoxide dismutase [cu-zn]: “Monomeric human CU,ZN superoxide dismutase, loops IV and VII deleted, apo form, mutant H43F”. X-ray diffraction, 15 pockets (best druggability 0.76). MolNFT v1 #86654 on GenesisL1: 3D structure…
- PDB
- 4BD4
- Type
- protein
- Length
- 941 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase [cu-zn]
- EC
- 1.15.1.1
- UniProt
- P00441
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 8 distinct chains · 0% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 109 | 0% helix, 50% strand | P00441 |
| C | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 108 | 0% helix, 53% strand | P00441 |
| D | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 104 | 0% helix, 52% strand | P00441 |
| E | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 104 | 0% helix, 54% strand | P00441 |
| F | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 102 | 0% helix, 51% strand | P00441 |
| G | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 107 | 0% helix, 50% strand | P00441 |
| H | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 100 | 0% helix, 52% strand | P00441 |
| I | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 98 | 0% helix, 53% strand | P00441 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, E, B, F, C, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.76 | 0.99 | 21 | GOL |
| 2 | 68 | 0.74 | 0.98 | 21 | GOL |
| 3 | 64 | 0.73 | 0.98 | 21 | GOL |
| 4 | 539 | 0.73 | 0.81 | 56 | empty |
| 5 | 450 | 0.69 | 0.80 | 37 | empty |
Interfaces
13 interfaces between chains.
- C–G · 889 Ų buried · 23 hydrogen bonds · protein-protein
- B–F · 854 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 837 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 438 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 428 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4BD4 · Monomeric Human Cu,Zn Superoxide dismutase, loops IV and VII deleted, apo form, mutant… · 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 4BD4 · PDBe 4BD4 · UniProt P00441
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