MolNFT v1 · #84289 · protein
Crystal structure of PBP2A from mrsa in complex with peptidoglycan analogue at allosteric
3ZG5 · Penicillin binding protein 2 prime: “Crystal structure of PBP2A from mrsa in complex with peptidoglycan analogue at allosteric”. X-ray diffraction, 3 ligands (AMV, CD, CL), 16 pockets (best druggability 0.75). MolNFT v1 #84289 on…
- 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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