Research workbench
Crystal structure of acinetobacter baumannii PBP1A in complex with penicillin G
Analyse Crystal structure of acinetobacter baumannii PBP1A in complex with penicillin G in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UDI
- Type
- protein
- Length
- 1,201 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 1A
- UniProt
- G1C794
- Ligands
- PNM
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 1A | protein | 600 | 37% helix, 19% strand | G1C794 |
| B | Penicillin-binding protein 1A | protein | 601 | 37% helix, 20% strand | G1C794 |
Ligands and binding sites
- PNM · Open form - penicillin G · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.78 | 0.95 | 30 | empty |
| 2 | 343 | 0.72 | 0.85 | 37 | empty |
| 3 | 247 | 0.54 | 0.77 | 38 | PNM |
| 4 | 218 | 0.51 | 0.76 | 33 | PNM |
| 5 | 182 | 0.50 | 0.77 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 2683 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 3UDI · Crystal structure of Acinetobacter baumannii PBP1a in complex with penicillin G · 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 G1C794
- Elsewhere: RCSB PDB 3UDI · PDBe 3UDI · UniProt G1C794
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