Research workbench
2.6 ångström resolution crystal structure of penicillin-binding protein 1A from haemophilus influenzae
Analyse 2.6 ångström resolution crystal structure of penicillin-binding protein 1A from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U2G
- Type
- protein
- Length
- 1,338 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 1A
- EC
- 2.4.2.-, 3.4.-.-
- UniProt
- P31776
- Ligands
- SO4, CL
- Pockets
- 18 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 1A (EC 2.4.2.-, 3.4.-.-) | protein | 668 | 33% helix, 20% strand | P31776 |
| B | Penicillin-binding protein 1A (EC 2.4.2.-, 3.4.-.-) | protein | 670 | 34% helix, 20% strand | P31776 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 16 copies · chains A, B
- CL · Chloride ion · ion · 9 copies · chains A, B
- GOL · Glycerol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.60 | 0.81 | 33 | empty |
| 2 | 217 | 0.59 | 0.80 | 34 | empty |
| 3 | 119 | 0.56 | 0.84 | 25 | CL |
| 4 | 358 | 0.56 | 0.75 | 30 | empty |
| 5 | 75 | 0.54 | 0.86 | 20 | CL |
Interfaces
1 interface between chains.
- A–B · 390 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 5U2G · 2.6 Angstrom Resolution Crystal Structure of Penicillin-Binding Protein 1A from… · the same entry in another collection · chain A against A, TM-score 1.00
- P31776 · AlphaFold monomer V2.0 prediction for penicillin-binding protein 1A (P31776) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P31776
- Elsewhere: RCSB PDB 5U2G · PDBe 5U2G · UniProt P31776
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