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Crystal structure of an mbp-der P 7 fusion protein

Analyse Crystal structure of an mbp-der P 7 fusion protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3H4Z
Type: protein
Length: 1,683 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Maltose-binding periplasmic protein fused with allergen DERP7
UniProt: P0AEX9, P49273
Ligands: GLC, NA
Pockets: 19 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Maltose-binding periplasmic protein fused with allergen DERP7	protein	568	39% helix, 27% strand	P0AEX9, P49273
B	Maltose-binding periplasmic protein fused with allergen DERP7	protein	563	39% helix, 26% strand	P0AEX9, P49273
C	Maltose-binding periplasmic protein fused with allergen DERP7	protein	552	39% helix, 26% strand	P0AEX9, P49273

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 6 copies · chains A, B, C
NA · Sodium ion · metal · chains A

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

Pockets

19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	711	0.77	0.82	77	GLC
2	473	0.74	0.83	48	GLC
3	450	0.71	0.81	42	GLC
4	514	0.67	0.78	63	NA
5	291	0.54	0.75	38	empty

Interfaces

3 interfaces between chains.

B–C · 416 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 247 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 151 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3H4Z · Crystal Structure of an MBP-Der p 7 fusion protein · the same entry in another collection · chain A against A, TM-score 1.00
P49273 · AlphaFold monomer V2.0 prediction for mite allergen der P 7 (P49273) · a predicted model of the same protein · chain A against A, TM-score 0.35

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 P0AEX9
Every structure of UniProt P49273
Elsewhere: RCSB PDB 3H4Z · PDBe 3H4Z · UniProt P0AEX9 · UniProt P49273

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