MolNFT v1 · #44150 · protein

High resolution structure of red abalone lysin dimer

2LYN · Sperm lysin: “High resolution structure of red abalone lysin dimer”. X-ray diffraction, 7 pockets (best druggability 0.79). MolNFT v1 #44150 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2LYN
Type: protein
Length: 510 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sperm lysin
UniProt: P04552
Pockets: 7 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 71% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sperm lysin	protein	130	72% helix, 0% strand	P04552
B	Sperm lysin	protein	125	70% helix, 0% strand	P04552
C	Sperm lysin	protein	127	72% helix, 0% strand	P04552
D	Sperm lysin	protein	128	71% helix, 0% strand	P04552

Pockets

7 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	123	0.79	0.97	24	empty
2	113	0.79	0.97	24	empty
3	987	0.73	0.76	63	empty
4	78	0.51	0.84	17	empty
5	64	0.50	0.85	19	empty

Interfaces

6 interfaces between chains.

A–D · 1012 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 920 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 885 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 298 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 203 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2LYN · High resolution structure of red abalone lysin dimer · the same entry in another collection · chain C against C, TM-score 1.00
P04552 · AlphaFold monomer V2.0 prediction for egg-lysin (P04552) · a predicted model of the same protein · chain B 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
Elsewhere: RCSB PDB 2LYN · PDBe 2LYN · UniProt P04552

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