MolNFT v1 · #140444 · protein

Crystal structure of lp-11/N44

5YB2 · Envelope glycoprotein: “Crystal structure of lp-11/N44”. X-ray diffraction, 3 pockets (best druggability 0.64). MolNFT v1 #140444 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YB2
Type: protein
Length: 411 residues
Chains: 14
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Envelope glycoprotein; Lp-11
UniProt: Q1HMR5
Pockets: 3 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 85% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, D, B, A, M	Envelope glycoprotein	protein	36	86% helix, 0% strand	Q1HMR5
F, C	Envelope glycoprotein	protein	35	89% helix, 0% strand	Q1HMR5
H, G, I, K, J, L, P	Lp-11	protein	23	78% helix, 0% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	561	0.64	0.75	57	empty
2	141	0.49	0.79	17	empty
3	99	0.48	0.81	18	empty

Interfaces

30 interfaces between chains.

A–C · 714 Å² buried · 3 hydrogen bonds · protein-protein
D–F · 712 Å² buried · 5 hydrogen bonds · protein-protein
E–D · 697 Å² buried · 3 hydrogen bonds · protein-protein
B–A · 694 Å² buried · 3 hydrogen bonds · protein-protein
E–F · 691 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5YB2 · Crystal structure of LP-11/N44 · the same entry in another collection · chain E against E, 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 Q1HMR5
Elsewhere: RCSB PDB 5YB2 · PDBe 5YB2 · UniProt Q1HMR5

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