MolNFT v1 · #151900 · protein
Crystal structure of tp domain from chlamydia trachomatis penicillin- binding protein 3 in complex with amoxicillin
6I1F · Penicillin-binding PROTEIN,PENICILLIN-binding protein: “Crystal structure of tp domain from chlamydia trachomatis penicillin- binding protein 3 in complex with…”. X-ray diffraction, 1 ligand (AXL), 5 pockets (best druggability…
- PDB
- 6I1F
- Type
- protein
- Length
- 685 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
- AXL
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding PROTEIN,PENICILLIN-binding protein (EC 2.4.1.129) | protein | 343 | 33% helix, 20% strand | A0A0E9FXJ8 |
| B | Penicillin-binding PROTEIN,PENICILLIN-binding protein (EC 2.4.1.129) | protein | 342 | 33% helix, 22% strand | A0A0E9FXJ8 |
Ligands and binding sites
- AXL · 2-{1-[2-amino-2-(4-hydroxy-phenyl)-acetylamino]-2-oxo-ethyl}-5,5-dimethyl-thiazolidine-4-carboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.72 | 0.97 | 20 | empty |
| 2 | 682 | 0.69 | 0.77 | 83 | AXL |
| 3 | 197 | 0.58 | 0.80 | 21 | empty |
| 4 | 245 | 0.50 | 0.75 | 34 | empty |
| 5 | 193 | 0.49 | 0.76 | 29 | AXL |
Interfaces
1 interface between chains.
- A–B · 1084 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6I1F · 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 6I1F · PDBe 6I1F · UniProt A0A0E9FXJ8
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