Research workbench
Crystal structure of tp domain from chlamydia trachomatis penicillin- binding protein 3 in complex with meropenem
Analyse Crystal structure of tp domain from chlamydia trachomatis penicillin- binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I1H
- Type
- protein
- Length
- 676 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding PROTEIN,PENICILLIN-binding protein
- EC
- 2.4.1.129
- UniProt
- A0A0E9FXJ8
- Ligands
- MER
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding PROTEIN,PENICILLIN-binding protein (EC 2.4.1.129) | protein | 340 | 33% helix, 21% strand | A0A0E9FXJ8 |
| B | Penicillin-binding PROTEIN,PENICILLIN-binding protein (EC 2.4.1.129) | protein | 336 | 35% helix, 21% strand | A0A0E9FXJ8 |
Ligands and binding sites
- MER · (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.72 | 0.96 | 21 | empty |
| 2 | 798 | 0.72 | 0.78 | 88 | MER |
| 3 | 243 | 0.53 | 0.76 | 33 | MER |
| 4 | 151 | 0.44 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 865 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6I1H · Crystal structure of TP domain from Chlamydia trachomatis Penicillin-Binding Protein 3 in… · 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 A0A0E9FXJ8
- Elsewhere: RCSB PDB 6I1H · PDBe 6I1H · UniProt A0A0E9FXJ8
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