SMTL ID : 8q5u.1

Endoglycosidase S2 in complex with IgG1 Fc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-3-3-mer

Ligands

1 x NAG- NAG- BMA- MAN- NAG- MAN- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-MAN-NAG-FUC.1: 35 residues within 4Å: Chain A: E.74, N.77, S.78 Chain B: Y.34, R.36, W.38, H.39, Q.51, H.52, F.70, H.71, D.72, H.73, T.102, I.103, G.104, A.148, L.150, H.151, F.153, D.190, T.192, R.213, Q.214, Y.215, Y.216, Q.219, E.252, E.253, S.254, A.255, S.256, N.259, W.261, Y.303 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.72, B:H.73, B:E.252, B:Y.303, B:Q.214, B:Y.216, B:Q.219, B:H.71, B:H.71

1 x NAG- NAG- BMA- MAN- NAG- MAN- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-MAN-FUC.2: 34 residues within 4Å: Chain C: E.74, N.77 Chain E: Y.34, R.36, W.38, H.39, F.70, H.71, D.72, H.73, T.102, I.103, G.104, A.148, L.150, H.151, F.153, D.190, T.192, R.213, Q.214, Y.215, Y.216, Q.219, S.249, E.252, E.253, S.254, A.255, S.256, G.258, N.259, W.261, Y.303 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:D.72, E:H.73, E:Y.303, E:Y.216, E:Q.219, E:Q.219, E:R.36, E:W.38, E:E.253, E:E.253, E:N.259, E:H.71, E:H.71, E:G.104 Hydrophobic interactions: E:F.70

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: L.212, H.213, N.214, H.215 Chain B: W.676 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.214 GOL.7: 4 residues within 4Å: Chain B: S.292, E.383, R.384, K.407 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.383, B:K.407 Water bridges: B:R.384 GOL.13: 3 residues within 4Å: Chain F: M.32, N.214, Y.216 No protein-ligand interaction detected (PLIP) GOL.14: 5 residues within 4Å: Chain D: W.676 Chain F: L.212, H.213, N.214, H.215 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:H.213, F:N.214

5 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 7 residues within 4Å: Chain B: D.434, Q.456, T.457, D.459, K.551, R.552 Ligands: PGE.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.551, B:K.551 PGE.5: 9 residues within 4Å: Chain B: Y.519, Y.520, Q.522, V.549, T.550, K.551, R.552, N.553 Ligands: PGE.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.522, B:K.551 PGE.6: 8 residues within 4Å: Chain B: K.650, I.652, D.685, L.729, E.730, R.737, R.770, Y.771 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.650, B:D.685, B:R.770 PGE.10: 4 residues within 4Å: Chain E: H.468, T.470, H.501, Q.502 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:H.501 PGE.11: 8 residues within 4Å: Chain E: T.457, Y.519, Q.522, V.549, T.550, K.551, R.552, N.553 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.522, E:N.553

3 x CA: CALCIUM ION(Non-covalent)

CA.8: 8 residues within 4Å: Chain B: K.663, D.666, E.668, K.669, S.670, D.671, T.788, E.789 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:K.663, B:D.666, B:E.668, B:T.788 CA.9: 9 residues within 4Å: Chain D: K.663, I.664, D.666, E.668, K.669, S.670, D.671, T.788, E.789 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:K.663, D:D.666, D:E.668, D:T.788, D:E.789 CA.12: 9 residues within 4Å: Chain E: K.663, I.664, D.666, E.668, K.669, S.670, D.671, T.788, E.789 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:K.663, E:D.666, E:E.668, E:T.788

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sudol, A.S.L. et al., The IgG-specific endoglycosidases EndoS and EndoS2 are distinguished by conformation and antibody recognition. J.Biol.Chem. (2024)

Release Date

2024-04-17

Peptides

Uncharacterized protein DKFZp686C11235: ACF
Endo-beta-N-acetylglucosaminidase: BDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

F
B

B
D

D
E

E
F

Uncharacterized protein DKFZp686C11235

Endo-beta-N-acetylglucosaminidase