MolNFT v1 · #122205 · protein

Crystal structure of red abalone egg verl repeat 3 in complex with sperm lysin at 1.7 a resolution (crystal form I)

5IIA · Egg-lysin: “Crystal structure of red abalone egg verl repeat 3 in complex with sperm lysin at 1.7 a resolution (crystal…”. X-ray diffraction, 1 ligand (NAG), 11 pockets (best druggability 0.75). MolNFT v1 #122205 on GenesisL1: 3D…

PDB: 5IIA
Type: protein
Length: 922 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
Pockets: 11 · best druggability 0.75

Structure

x-ray diffraction · 6 distinct chains · 27% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	Egg-lysin	protein	125	73% helix, 0% strand	P04552
B	Vitelline envelope sperm lysin receptor	protein	107	0% helix, 62% strand	Q8WR62
D	Vitelline envelope sperm lysin receptor	protein	107	0% helix, 58% strand	Q8WR62
F	Vitelline envelope sperm lysin receptor	protein	105	0% helix, 63% strand	Q8WR62
G	Egg-lysin	protein	126	72% helix, 0% strand	P04552
H	Vitelline envelope sperm lysin receptor	protein	102	0% helix, 62% strand	Q8WR62

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains B, D, F, H

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

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	781	0.75	0.80	65	empty
2	153	0.58	0.82	18	NAG
3	210	0.58	0.80	39	empty
4	206	0.54	0.78	22	empty
5	63	0.47	0.84	24	empty

Interfaces

8 interfaces between chains.

A–B · 1212 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 1211 Å² buried · 9 hydrogen bonds · protein-protein
G–H · 1183 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 1180 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 778 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 8 glycan (disulfide, N-glycosylation).

Compared structures

5IIA · Crystal structure of red abalone egg VERL repeat 3 in complex with sperm lysin at 1.7 A… · 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 C 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 5IIA · PDBe 5IIA · UniProt P04552 · UniProt Q8WR62

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