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Crystal structure of Y.PESTIS oligo peptide binding protein oppa with tri-lysine ligand

Analyse Crystal structure of Y.PESTIS oligo peptide binding protein oppa with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2Z23
Type: protein
Length: 520 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Periplasmic oligopeptide-binding protein; Peptide (LYS)(LYS)(LYS)
UniProt: Q74TY5
Pockets: 3 · best druggability 0.31

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Periplasmic oligopeptide-binding protein	protein	517	35% helix, 22% strand	Q74TY5
B	Peptide (LYS)(LYS)(LYS)	protein	3	0% helix, 33% strand	—

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	67	0.31	0.74	18	empty
2	53	0.29	0.76	18	empty
3	67	0.27	0.72	19	empty

Interfaces

1 interface between chains.

A–B · 509 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

2Z23 · Crystal structure of Y.pestis oligo peptide binding protein OppA with tri-lysine ligand · the same entry in another collection · 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 Q74TY5
Elsewhere: RCSB PDB 2Z23 · PDBe 2Z23 · UniProt Q74TY5

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