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Structure of a lamprey variable lymphocyte receptor mutant in complex with a protein antigen

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PDB: 3G3B
Type: protein
Length: 1,065 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Variable lymphocyte receptor VLRB.2D; Lysozyme C
EC: 3.2.1.17
UniProt: P00698
Pockets: 7 · best druggability 0.78

Structure

x-ray diffraction · 8 distinct chains · 24% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Variable lymphocyte receptor VLRB.2D	protein	169	12% helix, 16% strand	—
B	Lysozyme C (EC 3.2.1.17)	protein	127	39% helix, 11% strand	P00698
C	Variable lymphocyte receptor VLRB.2D	protein	167	8% helix, 16% strand	—
D	Lysozyme C (EC 3.2.1.17)	protein	124	41% helix, 11% strand	P00698
E	Variable lymphocyte receptor VLRB.2D	protein	159	8% helix, 16% strand	—
F	Lysozyme C (EC 3.2.1.17)	protein	125	42% helix, 11% strand	P00698
G	Variable lymphocyte receptor VLRB.2D	protein	71	10% helix, 18% strand	—
H	Lysozyme C (EC 3.2.1.17)	protein	123	41% helix, 11% strand	P00698

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1164	0.78	0.80	97	empty
2	406	0.64	0.79	50	empty
3	187	0.56	0.80	28	empty
4	217	0.54	0.77	35	empty
5	178	0.51	0.78	32	empty

Interfaces

11 interfaces between chains.

A–B · 819 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 799 Å² buried · 13 hydrogen bonds · protein-protein
G–H · 784 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 780 Å² buried · 16 hydrogen bonds · protein-protein
B–H · 552 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 19 disulfide (disulfide).

Compared structures

3G3B · Structure of a lamprey variable lymphocyte receptor mutant in complex with a protein… · 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 P00698
Elsewhere: RCSB PDB 3G3B · PDBe 3G3B · UniProt P00698

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