Research workbench
Structure of penicillin binding protein 2A from methicillin resistant staphylococcus aureus strain 27R at 1.80 a resolution.
Analyse Structure of penicillin binding protein 2A from methicillin resistant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VQQ
- Type
- protein
- Length
- 1,260 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein meca, low-affinity
- UniProt
- Q2PF50
- Ligands
- CD, CL
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein meca, low-affinity | protein | 635 | 34% helix, 27% strand | Q2PF50 |
| B | Penicillin-binding protein meca, low-affinity | protein | 625 | 36% helix, 26% strand | Q2PF50 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 917 | 0.76 | 0.79 | 89 | CL, CD |
| 2 | 450 | 0.66 | 0.79 | 49 | empty |
| 3 | 379 | 0.63 | 0.78 | 39 | empty |
| 4 | 181 | 0.53 | 0.79 | 21 | empty |
| 5 | 232 | 0.52 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1440 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 1VQQ · Structure of Penicillin binding protein 2a from methicillin resistant Staphylococcus… · 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 Q2PF50
- Elsewhere: RCSB PDB 1VQQ · PDBe 1VQQ · UniProt Q2PF50
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