Research workbench
Crystal structure of LYS154ARG mutant of mature apha of S. typhimurium
Analyse Crystal structure of LYS154ARG mutant of mature apha of S. typhimurium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z88
- Type
- protein
- Length
- 837 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apha protein
- EC
- 3.1.3.2
- UniProt
- P58683
- Ligands
- MG
- Pockets
- 14 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Apha protein (EC 3.1.3.2) | protein | 208 | 36% helix, 17% strand | P58683 |
| B, C | Apha protein (EC 3.1.3.2) | protein | 209 | 37% helix, 17% strand | P58683 |
| D | Apha protein (EC 3.1.3.2) | protein | 211 | 36% helix, 17% strand | P58683 |
Ligands and binding sites
- MG · Magnesium 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
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 500 | 0.69 | 0.79 | 52 | empty |
| 2 | 292 | 0.64 | 0.81 | 41 | empty |
| 3 | 348 | 0.61 | 0.78 | 47 | MG |
| 4 | 197 | 0.55 | 0.79 | 24 | MG |
| 5 | 196 | 0.54 | 0.79 | 22 | MG |
Interfaces
6 interfaces between chains.
- A–B · 1382 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1346 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1003 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 987 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 643 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1Z88 · Crystal structure of Lys154Arg mutant of mature AphA of S. typhimurium · the same entry in another collection · chain D against D, TM-score 1.00
- P58683 · AlphaFold monomer V2.0 prediction for class B acid phosphatase (P58683) · a predicted model of the same protein · chain D 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 P58683
- Elsewhere: RCSB PDB 1Z88 · PDBe 1Z88 · UniProt P58683
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