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Lactococcal oppa complexed with an endogenous peptide in the closed conformation

Analyse Lactococcal oppa complexed with an endogenous peptide 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: 3DRF
Type: protein
Length: 547 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Oligopeptide-binding protein oppa; Endogenous peptide
UniProt: A2RJ53
Pockets: 5 · best druggability 0.89

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Oligopeptide-binding protein oppa	protein	539	31% helix, 24% strand	A2RJ53
B	Endogenous peptide	protein	8	0% helix, 25% strand	—

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	766	0.89	0.93	98	empty
2	83	0.73	0.96	24	empty
3	107	0.45	0.79	20	empty
4	94	0.40	0.77	20	empty
5	73	0.40	0.79	15	empty

Interfaces

1 interface between chains.

A–B · 724 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

3DRF · Lactococcal OppA complexed with an endogenous peptide 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 3DRF · PDBe 3DRF · UniProt A2RJ53

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