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Crystal structure of PBP2A from mrsa in complex with peptidoglycan analogue at allosteric
Analyse Crystal structure of PBP2A from mrsa in complex with peptidoglycan analogue at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZG5
- Type
- protein
- Length
- 1,282 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin binding protein 2 prime; Peptidoglycan analogue
- EC
- 3.4.16.4
- UniProt
- Q54113
- Ligands
- AMV, CD, CL
- Pockets
- 16 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Penicillin binding protein 2 prime (EC 3.4.16.4) | protein | 636 | 33% helix, 26% strand | Q54113 |
| C, D | Peptidoglycan analogue | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- AMV · methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside · ligand · 2 copies · chains A, C, B, D
- CD · Cadmium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.75 | 0.79 | 76 | CL, CD |
| 2 | 103 | 0.67 | 0.91 | 19 | empty |
| 3 | 331 | 0.63 | 0.79 | 41 | AMV |
| 4 | 368 | 0.61 | 0.78 | 42 | empty |
| 5 | 182 | 0.57 | 0.81 | 34 | AMV |
Interfaces
3 interfaces between chains.
- A–B · 1615 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 391 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 373 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 d-amino, 2 modified (covalent ligand, D-amino acid, nonstandard).
Compared structures
- 3ZG5 · Crystal structure of PBP2a from MRSA in complex with peptidoglycan analogue at allosteric · 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 Q54113
- Elsewhere: RCSB PDB 3ZG5 · PDBe 3ZG5 · UniProt Q54113
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