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Crystal structure of mada-3

Analyse Crystal structure of mada-3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7E2V
Type: protein
Length: 977 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mada-3
Ligands: FAD, NAG
Pockets: 8 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mada-3	protein	500	35% helix, 22% strand	—
B	Mada-3	protein	477	35% helix, 22% strand	—

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1002	0.82	0.83	92	FAD
2	642	0.80	0.84	68	FAD
3	431	0.59	0.75	45	empty
4	298	0.54	0.76	40	empty
5	236	0.48	0.74	38	empty

Interfaces

1 interface between chains.

A–B · 861 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

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

Compared structures

7E2V · Crystal structure of MaDA-3 · 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
Elsewhere: RCSB PDB 7E2V · PDBe 7E2V

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