Research workbench
E. COLI PBP1B in complex with acyl-centa and moenomycin
Analyse E. COLI PBP1B in complex with acyl-centa and moenomycin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HLD
- Type
- protein
- Length
- 649 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 1B
- EC
- 2.4.1.129, 3.4.-.-
- UniProt
- P02919
- Ligands
- 63V, M0E
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 1B (EC 2.4.1.129, 3.4.-.-) | protein | 649 | 37% helix, 20% strand | P02919 |
Ligands and binding sites
- 63V · (2S)-5-methylidene-2-{(1R)-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid · ligand · chains A
- M0E · Moenomycin · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 489 | 0.73 | 0.82 | 45 | empty |
| 2 | 374 | 0.68 | 0.81 | 46 | empty |
| 3 | 258 | 0.53 | 0.76 | 26 | empty |
| 4 | 221 | 0.50 | 0.76 | 28 | 63V |
| 5 | 111 | 0.50 | 0.81 | 18 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
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
- Elsewhere: RCSB PDB 5HLD · PDBe 5HLD · UniProt P02919
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