MolNFT v1 · #16285 · protein

Helix C deletion mutant of bm-40 fs-ec domain pair

1NUB · Basement membrane protein bm-40: “Helix C deletion mutant of bm-40 fs-ec domain pair”. X-ray diffraction, 2 ligands (NAG, CA), 12 pockets (best druggability 0.54). MolNFT v1 #16285 on GenesisL1: 3D structure, binding sites and…

PDB: 1NUB
Type: protein
Length: 452 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Basement membrane protein bm-40
UniProt: P09486
Ligands: NAG, CA
Pockets: 12 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Basement membrane protein bm-40	protein	226	46% helix, 10% strand	P09486

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
CA · Calcium ion · metal · 6 copies · chains A, B

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

Pockets

12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	204	0.54	0.78	20	empty
2	197	0.51	0.77	20	empty
3	94	0.48	0.81	19	empty
4	97	0.46	0.80	18	empty
5	81	0.34	0.75	20	empty

Interfaces

1 interface between chains.

A–B · 885 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

1NUB · Helix C deletion mutant of bm-40 fs-ec domain pair · the same entry in another collection · chain A against A, TM-score 1.00
P09486 · AlphaFold monomer V2.0 prediction for sparc (P09486) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 P09486
Elsewhere: RCSB PDB 1NUB · PDBe 1NUB · UniProt P09486

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