MolNFT v1 · #62819 · protein
Crystal structure of penicillin-binding protein 2 from neisseria gonorrhoeae
3EQU: “Crystal structure of penicillin-binding protein 2 from neisseria gonorrhoeae”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.54). MolNFT v1 #62819 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3EQU
- Type
- protein
- Length
- 855 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 2
- EC
- 3.4.16.4
- UniProt
- P08149
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 2 (EC 3.4.16.4) | protein | 429 | 34% helix, 24% strand | P08149 |
| B | Penicillin-binding protein 2 (EC 3.4.16.4) | protein | 426 | 33% helix, 23% strand | P08149 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.54 | 0.74 | 34 | SO4 |
| 2 | 99 | 0.52 | 0.83 | 21 | empty |
| 3 | 142 | 0.47 | 0.78 | 24 | empty |
| 4 | 132 | 0.44 | 0.76 | 23 | empty |
| 5 | 53 | 0.41 | 0.82 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 238 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered, phosphorylation).
Compared structures
- 3EQU · Crystal structure of penicillin-binding protein 2 from Neisseria gonorrhoeae · the same entry in another collection · chain A against A, TM-score 1.00
- P08149 · AlphaFold monomer V2.0 prediction for probable peptidoglycan D,D-transpeptidase pena… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P08149
- Elsewhere: RCSB PDB 3EQU · PDBe 3EQU · UniProt P08149
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