MolNFT v1 · #129391 · protein

Penicillin-binding protein 2X (PBP2X) from streptococcus pneumoniae in complex with cefepime

5OJ0: “Penicillin-binding protein 2X (PBP2X) from streptococcus pneumoniae in complex with cefepime”. X-ray diffraction, 1 ligand (9WT), 8 pockets (best druggability 0.74). MolNFT v1 #129391 on GenesisL1: 3D structure, binding sites and…

PDB: 5OJ0
Type: protein
Length: 658 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Penicillin-binding protein 2X
UniProt: P59676
Ligands: 9WT
Pockets: 8 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 29% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Penicillin-binding protein 2X	protein	658	29% helix, 23% strand	P59676

Ligands and binding sites

9WT · Cefepime · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	372	0.74	0.85	47	empty
2	480	0.66	0.78	41	9WT
3	64	0.53	0.87	21	empty
4	89	0.49	0.82	20	empty
5	179	0.44	0.74	28	empty

Compared structures

5OJ0 · Penicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
P59676 · AlphaFold monomer V2.0 prediction for penicillin-binding protein 2X (P59676) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P59676
Elsewhere: RCSB PDB 5OJ0 · PDBe 5OJ0 · UniProt P59676

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