PDBsum entry 2agd

Ligand/metal interactions

PDB id

2agd


	3 instances of ligand highlighted
	BMA-MAN-NAG

Ligands

BMA-MAN-NAG ×3

BMA 1(D) to NAG 3(D)

SO4 ×16

UDH ×3

GOL ×8

DIO

MES

Metals

_MN ×3

MN 400(A)

Ligand BMA-MAN-NAG

BMA - Beta-D-Mannopyranose [Beta-D-Mannose; d-Mannose; mannose] Formula: C₆H₁₂O₆

MAN - Alpha-D-Mannopyranose [Alpha-D-Mannose; d-Mannose; mannose] Formula: C₆H₁₂O₆

NAG - 2-Acetamido-2-Deoxy-Beta-D-Glucopyranose [N-Acetyl-Beta-D-Glucosamine; 2-Acetamido-2-Deoxy-Beta- D-Glucose; 2-Acetamido-2-Deoxy-D-Glucose; 2-Acetamido- 2-Deoxy-Glucose; n-Acetyl-D-Glucosamine] Formula: C₈H₁₅NO₆

Validation of ligand annotation

Per Residue Validation

	Atoms				Missing		Incorrect Chiral Centres
Residue	Dic.	Struc.	Link	Subs.	Atoms	Rings	Planar	High	C	Other
BMA 1(D)	12	12	0	0	Complete		Chiral checks - OK
MAN 2(D)	12	12	1	0	Complete		Chiral checks - OK
NAG 3(D)	15	15	1	0	Complete		Chiral checks - OK

Additional Information

Validation carried out using MotiveValidator. Full validation report can be found in Validator^DB.

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Het Group NAG matches this enzyme's reactant N-acetyl-D-glucosamine with similarity 93.33%

LIGPLOT of interactions involving ligand BMA-MAN-NAG

List of
interactions

BMA 1(D) to NAG 3(D)

also representing 2 other equivalent ligands:
BMA 1(E) to NAG 3(E)
BMA 1(F) to NAG 3(F)