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Crystal structure of red abalone egg verl repeat 2 with linker in complex with sperm lysin at 1.8 a resolution

Analyse Crystal structure of red abalone egg verl repeat 2 with linker in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MR3
Type: protein
Length: 959 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Egg-lysin; Vitelline envelope sperm lysin receptor
UniProt: P04552, Q8WR62
Ligands: NAG, CL
Pockets: 14 · best druggability 0.83

Structure

x-ray diffraction · 8 distinct chains · 39% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Egg-lysin	protein	125	77% helix, 0% strand	P04552
B	Vitelline envelope sperm lysin receptor	protein	117	0% helix, 55% strand	Q8WR62
C	Egg-lysin	protein	127	76% helix, 0% strand	P04552
D	Vitelline envelope sperm lysin receptor	protein	110	0% helix, 60% strand	Q8WR62
E	Egg-lysin	protein	133	69% helix, 0% strand	P04552
F	Vitelline envelope sperm lysin receptor	protein	107	0% helix, 60% strand	Q8WR62
G	Egg-lysin	protein	129	71% helix, 0% strand	P04552
H	Vitelline envelope sperm lysin receptor	protein	111	0% helix, 59% strand	Q8WR62

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, D, F, H
CL · Chloride ion · ion · 2 copies · chains B, F
GOL · Glycerol · additive · 12 copies · chains A, B, H, D, C, F, E
PGE · Triethylene glycol · additive · 2 copies · chains A, G

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	801	0.83	0.86	87	PGE
2	509	0.76	0.83	53	GOL
3	618	0.76	0.82	63	GOL
4	354	0.74	0.85	51	GOL
5	496	0.72	0.81	46	empty

Interfaces

13 interfaces between chains.

G–H · 1252 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1226 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 1223 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 1182 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 951 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

5MR3 · Crystal structure of red abalone egg VERL repeat 2 with linker in complex with sperm… · the same entry in another collection · chain H against H, TM-score 1.00
P04552 · AlphaFold monomer V2.0 prediction for egg-lysin (P04552) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P04552
Every structure of UniProt Q8WR62
Elsewhere: RCSB PDB 5MR3 · PDBe 5MR3 · UniProt P04552 · UniProt Q8WR62

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