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Lactococcal oppa complexed with bradykinin in the closed conformation

Analyse Lactococcal oppa complexed with bradykinin in the closed conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3DRG
Type: protein
Length: 571 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Oligopeptide-binding protein oppa; Bradykinin
UniProt: A2RJ53
Ligands: CL
Pockets: 7 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Oligopeptide-binding protein oppa	protein	562	28% helix, 23% strand	A2RJ53
B	Bradykinin	protein	9	0% helix, 22% strand	—

Ligands and binding sites

CL · Chloride ion · ion · chains A

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

Pockets

7 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	963	0.87	0.88	64	empty
2	189	0.81	0.96	38	empty
3	88	0.76	0.98	24	empty
4	92	0.42	0.78	19	empty
5	152	0.41	0.74	27	empty

Interfaces

1 interface between chains.

A–B · 944 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

3DRG · Lactococcal OppA complexed with bradykinin in the closed conformation · 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 A2RJ53
Elsewhere: RCSB PDB 3DRG · PDBe 3DRG · UniProt A2RJ53

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