MolNFT v1 · #121100 · protein
E. COLI PBP1B in complex with acyl-cephalexin and moenomycin
5HLA · Penicillin-binding protein 1B: “E. COLI PBP1B in complex with acyl-cephalexin and moenomycin”. X-ray diffraction, 2 ligands (63U, M0E), 7 pockets (best druggability 0.73). MolNFT v1 #121100 on GenesisL1: 3D structure, binding sites…
- PDB
- 5HLA
- Type
- protein
- Length
- 697 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
- 63U, M0E
- Pockets
- 7 · 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 | 697 | 37% helix, 20% strand | P02919 |
Ligands and binding sites
- 63U · (2S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5-methyl-3,6-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
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 365 | 0.73 | 0.84 | 37 | empty |
| 2 | 485 | 0.67 | 0.78 | 41 | empty |
| 3 | 322 | 0.65 | 0.81 | 38 | empty |
| 4 | 93 | 0.53 | 0.84 | 18 | empty |
| 5 | 237 | 0.48 | 0.74 | 28 | 63U |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5HLA · E. coli PBP1b in complex with acyl-cephalexin and moenomycin · 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 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 P02919
- Elsewhere: RCSB PDB 5HLA · PDBe 5HLA · UniProt P02919
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