Research workbench
Crystal structure of LYS154ASN mutant of mature apha of S. typhimurium
Analyse Crystal structure of LYS154ASN 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
- 2AUT
- Type
- protein
- Length
- 836 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apha
- EC
- 3.1.3.2
- UniProt
- P58683
- Ligands
- MG, NA, PO4
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Apha (EC 3.1.3.2) | protein | 208 | 36% helix, 17% strand | P58683 |
| B, C | Apha (EC 3.1.3.2) | protein | 209 | 36% helix, 17% strand | P58683 |
| D | Apha (EC 3.1.3.2) | protein | 210 | 36% helix, 17% strand | P58683 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains D
- PO4 · Phosphate ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.70 | 0.80 | 57 | empty |
| 2 | 317 | 0.65 | 0.81 | 47 | NA, PO4 |
| 3 | 358 | 0.62 | 0.78 | 43 | MG |
| 4 | 351 | 0.62 | 0.78 | 46 | empty |
| 5 | 288 | 0.60 | 0.78 | 38 | MG |
Interfaces
6 interfaces between chains.
- A–B · 1385 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1366 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1000 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 988 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 647 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2AUT · Crystal structure of Lys154Asn 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 2AUT · PDBe 2AUT · UniProt P58683
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