Research workbench

Structure of MDR3_DD-C363G with mbp tag

Analyse Structure of MDR3_DD-C363G with mbp tag in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ZNY
Type: protein
Length: 1,801 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Maltose-binding periplasmic PROTEIN,TUMOR necrosis factor receptor superfamily, member 25
UniProt: P0AEX9, B1AWN9
Ligands: SO4
Pockets: 14 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 51% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Maltose-binding periplasmic PROTEIN,TUMOR necrosis factor receptor superfamily, member 25	protein	448	50% helix, 17% strand	P0AEX9, B1AWN9
B, C	Maltose-binding periplasmic PROTEIN,TUMOR necrosis factor receptor superfamily, member 25	protein	450	51% helix, 17% strand	P0AEX9, B1AWN9
D	Maltose-binding periplasmic PROTEIN,TUMOR necrosis factor receptor superfamily, member 25	protein	453	51% helix, 17% strand	P0AEX9, B1AWN9

Ligands and binding sites

SO4 · Sulfate ion · ion · 27 copies · chains A, C, B, D

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

Pockets

14 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	1035	0.79	0.80	86	SO4
2	945	0.76	0.79	94	SO4
3	880	0.74	0.78	81	SO4
4	782	0.70	0.77	64	SO4
5	168	0.69	0.88	34	SO4

Interfaces

6 interfaces between chains.

B–D · 1367 Å² buried · 27 hydrogen bonds · protein-protein
A–C · 1310 Å² buried · 25 hydrogen bonds · protein-protein
A–D · 602 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 535 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 157 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5ZNY · Structure of mDR3_DD-C363G with MBP tag · 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
Every structure of UniProt B1AWN9
Elsewhere: RCSB PDB 5ZNY · PDBe 5ZNY · UniProt P0AEX9 · UniProt B1AWN9

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