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1.8 ångström resolution crystal structure of dimerization and transpeptidase domains (residues 39-608) of penicillin-binding protein 1 from staphylococcus aureus.
Analyse 1.8 ångström resolution crystal structure of dimerization and transpeptidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TRO
- Type
- protein
- Length
- 1,011 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 1
- UniProt
- A0A0H2WVW5
- Ligands
- CL
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 1 | protein | 505 | 33% helix, 25% strand | A0A0H2WVW5 |
| B | Penicillin-binding protein 1 | protein | 506 | 32% helix, 25% strand | A0A0H2WVW5 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.80 | 0.83 | 94 | empty |
| 2 | 797 | 0.79 | 0.83 | 91 | empty |
| 3 | 144 | 0.70 | 0.90 | 29 | empty |
| 4 | 331 | 0.65 | 0.80 | 46 | empty |
| 5 | 323 | 0.64 | 0.80 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 1897 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 5TRO · 1.8 Angstrom Resolution Crystal Structure of Dimerization and Transpeptidase domains… · the same entry in another collection · chain A 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 A0A0H2WVW5
- Elsewhere: RCSB PDB 5TRO · PDBe 5TRO · UniProt A0A0H2WVW5
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