MolNFT v1 · #82413 · protein
Crystal structure of the full-length transglycosylase PBP1B from escherichia COLI
3VMA · Penicillin-binding protein 1B: “Crystal structure of the full-length transglycosylase PBP1B from escherichia COLI”. X-ray diffraction, 1 ligand (M0E), 9 pockets (best druggability 0.79). MolNFT v1 #82413 on GenesisL1: 3D structure…
- PDB
- 3VMA
- Type
- protein
- Length
- 708 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
- M0E
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 1B (EC 2.4.1.129, 3.4.-.-) | protein | 708 | 38% helix, 20% strand | P02919 |
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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 922 | 0.79 | 0.81 | 80 | empty |
| 2 | 298 | 0.69 | 0.83 | 34 | empty |
| 3 | 88 | 0.52 | 0.84 | 19 | empty |
| 4 | 249 | 0.49 | 0.74 | 36 | empty |
| 5 | 137 | 0.39 | 0.74 | 20 | empty |
Compared structures
- 3VMA · Crystal Structure of the Full-Length Transglycosylase PBP1b from Escherichia coli · 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 3VMA · PDBe 3VMA · UniProt P02919
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