Research workbench
Crystal structure of P104H mutant of sod-like protein from bacillus subtilis.
Analyse Crystal structure of P104H mutant of sod-like protein from bacillus subtilis. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XTL
- Type
- protein
- Length
- 608 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical superoxide dismutase-like protein yojm
- UniProt
- O31851
- Ligands
- ZN, CU
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C, D | Hypothetical superoxide dismutase-like protein yojm | protein | 152 | 0% helix, 41% strand | O31851 |
Ligands and binding sites
- ZN · Zinc ion · metal · 10 copies · chains B, A, C, D
- CU · Copper (II) ion · metal · 4 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 841 | 0.76 | 0.80 | 89 | empty |
| 2 | 787 | 0.76 | 0.80 | 78 | empty |
| 3 | 96 | 0.52 | 0.83 | 24 | empty |
| 4 | 53 | 0.27 | 0.75 | 13 | empty |
Interfaces
3 interfaces between chains.
- B–C · 482 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 476 Ų buried · 3 hydrogen bonds · protein-protein
- B–A · 438 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1XTL · Crystal structure of P104H mutant of SOD-like protein from Bacillus subtilis. · the same entry in another collection · chain B against B, TM-score 1.00
- O31851 · AlphaFold monomer V2.0 prediction for superoxide dismutase-like protein yojm (O31851) · 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 O31851
- Elsewhere: RCSB PDB 1XTL · PDBe 1XTL · UniProt O31851
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