Research workbench
Copper-reconstituted tomato chloroplast superoxide dismutase
Analyse Copper-reconstituted tomato chloroplast superoxide dismutase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S0P
- Type
- protein
- Length
- 985 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase [cu-zn], chloroplastic
- EC
- 1.15.1.1
- UniProt
- P14831
- Ligands
- CU
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 2% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, H | Superoxide dismutase [cu-zn], chloroplastic (EC 1.15.1.1) | protein | 124 | 2% helix, 48% strand | P14831 |
| B, D | Superoxide dismutase [cu-zn], chloroplastic (EC 1.15.1.1) | protein | 122 | 2% helix, 50% strand | P14831 |
| E, F | Superoxide dismutase [cu-zn], chloroplastic (EC 1.15.1.1) | protein | 123 | 2% helix, 49% strand | P14831 |
| G | Superoxide dismutase [cu-zn], chloroplastic (EC 1.15.1.1) | protein | 123 | 2% helix, 50% strand | P14831 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.72 | 0.81 | 52 | empty |
| 2 | 679 | 0.72 | 0.79 | 64 | empty |
| 3 | 529 | 0.67 | 0.78 | 65 | empty |
| 4 | 491 | 0.59 | 0.74 | 49 | empty |
| 5 | 199 | 0.58 | 0.81 | 23 | empty |
Interfaces
14 interfaces between chains.
- G–H · 693 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 692 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 687 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 687 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 375 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3S0P · Copper-reconstituted Tomato Chloroplast Superoxide Dismutase · the same entry in another collection · chain H against H, TM-score 1.00
- P14831 · AlphaFold monomer V2.0 prediction for superoxide dismutase [cu-zn], chloroplastic (P14831) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P14831
- Elsewhere: RCSB PDB 3S0P · PDBe 3S0P · UniProt P14831
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