MolNFT v1 · #161345 · protein

Crystal structure of nlppya P41A, D44N, N48E mutant

6QBD · 25 kda protein elicitor: “Crystal structure of nlppya P41A, D44N, N48E mutant”. X-ray diffraction, 1 ligand (MG), 2 pockets (best druggability 0.51). MolNFT v1 #161345 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6QBD
Type: protein
Length: 409 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 25 kda protein elicitor
UniProt: Q9SPD4
Ligands: MG
Pockets: 2 · best druggability 0.51

Structure

x-ray diffraction · 2 distinct chains · 19% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	25 kda protein elicitor	protein	203	20% helix, 35% strand	Q9SPD4
B	25 kda protein elicitor	protein	206	18% helix, 35% strand	Q9SPD4

Ligands and binding sites

MG · Magnesium ion · metal · 3 copies · chains A, B

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

Pockets

2 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	182	0.51	0.78	21	MG
2	90	0.41	0.78	20	MG

Interfaces

1 interface between chains.

A–B · 14 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

6QBD · Crystal structure of NLPPya P41A, D44N, N48E mutant · 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 Q9SPD4
Elsewhere: RCSB PDB 6QBD · PDBe 6QBD · UniProt Q9SPD4

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