MolNFT v1 · #123936 · protein
Structure of human SOD1 with T2D mutation
5K02 · Superoxide dismutase [cu-zn]: “Structure of human SOD1 with T2D mutation”. X-ray diffraction, 2 ligands (CU, ZN), 20 pockets (best druggability 0.78). MolNFT v1 #123936 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5K02
- Type
- protein
- Length
- 3,672 residues
- Chains
- 24
- 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
- CU, ZN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 153 | 6% helix, 40% strand | P00441 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
- ZN · Zinc ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 888 | 0.78 | 0.81 | 108 | empty |
| 2 | 1145 | 0.77 | 0.79 | 142 | empty |
| 3 | 1188 | 0.76 | 0.79 | 143 | empty |
| 4 | 596 | 0.76 | 0.82 | 69 | empty |
| 5 | 769 | 0.75 | 0.80 | 86 | empty |
Interfaces
57 interfaces between chains.
- A–B · 725 Ų buried · 4 hydrogen bonds · protein-protein
- Q–V · 696 Ų buried · 4 hydrogen bonds · protein-protein
- M–N · 685 Ų buried · 4 hydrogen bonds · protein-protein
- E–J · 684 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 398 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 5K02 · Structure of human SOD1 with T2D mutation · 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 5K02 · PDBe 5K02 · UniProt P00441
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