MolNFT v1 · #120173 · protein

Structure of mono-specific diabody

5GRU · Maltose-binding periplasmic protein: “Structure of mono-specific diabody”. X-ray diffraction, 9 pockets (best druggability 0.83). MolNFT v1 #120173 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GRU
Type: protein
Length: 828 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Maltose-binding periplasmic protein; Diabody protein
UniProt: P0AEX9
Pockets: 9 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 23% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Maltose-binding periplasmic protein	protein	360	46% helix, 19% strand	P0AEX9
H	Diabody protein	protein	240	5% helix, 50% strand	—
L	Diabody protein	protein	228	4% helix, 50% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	965	0.83	0.84	95	empty
2	441	0.64	0.78	50	empty
3	140	0.56	0.82	29	empty
4	61	0.45	0.83	16	empty
5	90	0.37	0.75	15	empty

Interfaces

3 interfaces between chains.

H–L · 2158 Å² buried · 17 hydrogen bonds · protein-protein
A–H · 866 Å² buried · 17 hydrogen bonds · protein-protein
A–L · 115 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5GRU · Structure of mono-specific diabody · 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 P0AEX9
Elsewhere: RCSB PDB 5GRU · PDBe 5GRU · UniProt P0AEX9

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