Research workbench
Crystal structure of Penicillin binding protein 3 (PBP3) from Mycobacterium tuerculosis, complexed with aztreonam
Analyse Crystal structure of Penicillin binding protein 3 (PBP3) from Mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KGU
- Type
- protein
- Length
- 448 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.106
- Source
- Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
- Molecule
- Penicillin-binding protein PbpB
- UniProt
- L0T911
- Ligands
- AZR, CO
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · resolution 2.106 · 1 distinct chain · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein PbpB | protein | 448 | 30% helix, 26% strand | L0T911 |
Ligands and binding sites
- AZR · 2-({[(1Z)-1-(2-amino-1,3-thiazol-4-yl)-2-oxo-2-{[(2S, 3S)-1-oxo-3-(sulfoamino)butan-2-yl]amino}ethylidene]amino}oxy)-2-methylpropanoic acid · ligand · chains A
- CO · Cobalt (II) ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.55 | 0.76 | 41 | AZR |
| 2 | 132 | 0.44 | 0.76 | 29 | empty |
| 3 | 58 | 0.29 | 0.75 | 16 | empty |
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 6KGU · Crystal structure of penicillin binding protein 3 (PBP3) from mycobacterium tuerculosis… · the same entry in another collection · chain A against A, TM-score 1.00
- L0T911 · AlphaFold monomer V2.0 prediction for penicillin-binding protein pbpb (L0T911) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 L0T911
- Elsewhere: RCSB PDB 6KGU · PDBe 6KGU · UniProt L0T911
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