Research workbench
Structure of E. COLI PBP1B with a ftsn peptide activating transglycosylase activity
Analyse Structure of E. COLI PBP1B with a ftsn peptide activating transglycosylase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YN0
- Type
- protein
- Length
- 702 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 1B; Cell division protein ftsn
- EC
- 2.4.1.129, 3.4.16.4
- UniProt
- P02919, P29131
- Ligands
- M0E
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 1B (EC 2.4.1.129, 3.4.16.4) | protein | 689 | 38% helix, 19% strand | P02919 |
| B | Cell division protein ftsn | protein | 13 | 85% helix, 0% strand | P29131 |
Ligands and binding sites
- M0E · Moenomycin · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.78 | 0.80 | 78 | empty |
| 2 | 385 | 0.68 | 0.81 | 47 | empty |
| 3 | 107 | 0.60 | 0.86 | 22 | empty |
| 4 | 263 | 0.50 | 0.75 | 42 | empty |
| 5 | 195 | 0.48 | 0.75 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 545 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6YN0 · Structure of E. coli PBP1b with a FtsN peptide activating transglycosylase activity · the same entry in another collection · chain A against A, TM-score 1.00
- P02919 · AlphaFold monomer V2.0 prediction for penicillin-binding protein 1B (P02919) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P29131 · AlphaFold monomer V2.0 prediction for cell division protein ftsn (P29131) · a predicted model of the same protein · chain B against A, TM-score 0.60
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 P02919
- Every structure of UniProt P29131
- Elsewhere: RCSB PDB 6YN0 · PDBe 6YN0 · UniProt P02919 · UniProt P29131
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