MolNFT v1 · #86872 · protein
Crystal structure of E. COLI penicillin binding protein 3, domain V88-S165
4BJQ · Penicillin binding protein transpeptidase domain protein: “Crystal structure of E. COLI penicillin binding protein 3, domain V88-S165”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.68). MolNFT v1 #86872 on…
- PDB
- 4BJQ
- Type
- protein
- Length
- 621 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin binding protein transpeptidase domain protein
- EC
- 2.4.1.129
- UniProt
- J2XFH0
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F | Penicillin binding protein transpeptidase domain protein (EC 2.4.1.129) | protein | 78 | 46% helix, 22% strand | J2XFH0 |
| E, G, H | Penicillin binding protein transpeptidase domain protein (EC 2.4.1.129) | protein | 77 | 45% helix, 22% strand | J2XFH0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, C, B, E, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 250 | 0.68 | 0.84 | 27 | empty |
| 2 | 243 | 0.64 | 0.82 | 27 | empty |
| 3 | 161 | 0.46 | 0.76 | 31 | empty |
| 4 | 198 | 0.45 | 0.74 | 38 | empty |
| 5 | 163 | 0.42 | 0.74 | 33 | empty |
Interfaces
8 interfaces between chains.
- B–E · 2424 Ų buried · 48 hydrogen bonds · protein-protein
- A–C · 2421 Ų buried · 53 hydrogen bonds · protein-protein
- D–H · 2328 Ų buried · 37 hydrogen bonds · protein-protein
- B–F · 749 Ų buried · 11 hydrogen bonds · protein-protein
- B–G · 500 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4BJQ · Crystal structure of E. coli penicillin binding protein 3, domain V88- S165 · the same entry in another collection · chain B against B, 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 J2XFH0
- Elsewhere: RCSB PDB 4BJQ · PDBe 4BJQ · UniProt J2XFH0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.