Research workbench
X-ray structure of the IRON/MANGANESE cambialistic superoxide dismutase from streptococcus mutans
Analyse X-ray structure of the IRON/MANGANESE cambialistic superoxide dismutase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YIP
- Type
- protein
- Length
- 810 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase [MN/FE]
- EC
- 1.15.1.1
- UniProt
- P09738
- Ligands
- FE
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Superoxide dismutase [MN/FE] (EC 1.15.1.1) | protein | 203 | 59% helix, 11% strand | P09738 |
| C | Superoxide dismutase [MN/FE] (EC 1.15.1.1) | protein | 201 | 57% helix, 11% strand | P09738 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 709 | 0.67 | 0.76 | 56 | empty |
| 2 | 255 | 0.62 | 0.81 | 23 | empty |
| 3 | 167 | 0.54 | 0.80 | 20 | empty |
| 4 | 266 | 0.54 | 0.76 | 37 | empty |
| 5 | 192 | 0.53 | 0.78 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 975 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 963 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 88 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 72 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 56 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4YIP · X-ray structure of the iron/manganese cambialistic superoxide dismutase from… · the same entry in another collection · chain B against B, TM-score 1.00
- P09738 · AlphaFold monomer V2.0 prediction for superoxide dismutase [MN/FE] (P09738) · a predicted model of the same protein · chain C 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 P09738
- Elsewhere: RCSB PDB 4YIP · PDBe 4YIP · UniProt P09738
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