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Crystal structure of galnac-T7 with MN2+

Analyse Crystal structure of galnac-T7 with MN2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6IWQ
Type: protein
Length: 3,276 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: N-acetylgalactosaminyltransferase 7
EC: 2.4.1.-
UniProt: Q86SF2
Ligands: MN
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	N-acetylgalactosaminyltransferase 7 (EC 2.4.1.-)	protein	546	26% helix, 25% strand	Q86SF2

Ligands and binding sites

MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	797	0.73	0.78	67	empty
2	606	0.71	0.79	63	MN
3	578	0.70	0.79	66	MN
4	534	0.70	0.79	63	MN
5	603	0.70	0.78	66	MN

Interfaces

9 interfaces between chains.

A–C · 1007 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 914 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 636 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 617 Å² buried · 5 hydrogen bonds · protein-protein
D–E · 373 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide (disulfide).

Compared structures

6IWQ · Crystal structure of GalNAc-T7 with Mn2+ · the same entry in another collection · chain F against F, TM-score 1.00
Q86SF2 · AlphaFold monomer V2.0 prediction for N-acetylgalactosaminyltransferase 7 (Q86SF2) · a predicted model of the same protein · chain E against A, TM-score 0.99

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 Q86SF2
Elsewhere: RCSB PDB 6IWQ · PDBe 6IWQ · UniProt Q86SF2

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