SMTL ID : 8kb7.1

Crystal structure of UDP/mannose-bound AGO61/beta-1,4-N-Acetylglucosaminyltransferase 2 (POMGNT2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

4 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.1: 16 residues within 4Å: Chain A: D.140, N.141, L.142, H.180, R.272, T.273, Q.274, N.275, R.276, L.301, E.302, G.324, A.325, Q.326, Y.425 Ligands: MAN.4 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:N.141, A:L.142, A:T.273, A:Q.274, A:N.275, A:R.276, A:E.302, A:A.325, A:Q.326, A:Q.326, A:Y.425 Salt bridges: A:R.272, A:R.272, A:R.276 pi-Cation interactions: A:R.272 UDP.6: 15 residues within 4Å: Chain B: D.140, N.141, L.142, H.180, R.272, Q.274, N.275, R.276, L.301, E.302, G.324, A.325, Q.326, Y.425 Ligands: MAN.8 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.141, B:L.142, B:R.272, B:R.272, B:Q.274, B:N.275, B:E.302, B:A.325, B:Q.326, B:Q.326 Salt bridges: B:R.276 pi-Cation interactions: B:R.272 UDP.10: 15 residues within 4Å: Chain C: D.140, N.141, L.142, H.180, R.272, Q.274, N.275, R.276, L.301, E.302, G.324, A.325, Q.326, Y.425 Ligands: MAN.13 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:N.141, C:L.142, C:R.272, C:Q.274, C:N.275, C:R.276, C:E.302, C:A.325, C:Q.326, C:Q.326, C:Y.425 Salt bridges: C:R.272, C:R.272, C:R.276 pi-Cation interactions: C:R.272 UDP.15: 15 residues within 4Å: Chain D: D.140, N.141, L.142, H.180, R.272, Q.274, N.275, R.276, L.301, E.302, G.324, A.325, Q.326, Y.425 Ligands: MAN.17 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:N.141, D:N.141, D:L.142, D:Q.274, D:N.275, D:E.302, D:A.325, D:Q.326, D:Q.326, D:Y.425 Salt bridges: D:R.272, D:R.272, D:R.276, D:R.276 pi-Cation interactions: D:R.272

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 4 residues within 4Å: Chain A: E.40, N.77, T.78 Chain B: R.247 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.78 NAG.3: 3 residues within 4Å: Chain A: L.186, K.252, N.254 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.186 Hydrogen bonds: A:N.254 NAG.7: 5 residues within 4Å: Chain A: Q.244, R.247 Chain B: E.40, N.77, T.78 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.78 NAG.11: 4 residues within 4Å: Chain C: E.40, N.77, T.78 Chain D: R.247 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:T.78 Hydrogen bonds: C:E.40 NAG.12: 1 residues within 4Å: Chain C: N.254 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.254 NAG.16: 4 residues within 4Å: Chain B: W.387 Chain D: S.483, Q.485, N.521 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.483, D:S.483, D:N.521

4 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.4: 7 residues within 4Å: Chain A: H.144, Y.223, Q.229, C.414, C.415, W.420 Ligands: UDP.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.141, A:Q.229, A:C.415 Salt bridges: A:H.144 MAN.8: 8 residues within 4Å: Chain B: N.141, H.144, Y.223, Q.229, C.414, C.415, W.420 Ligands: UDP.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.141, B:Q.229, B:C.415 Salt bridges: B:H.144 MAN.13: 7 residues within 4Å: Chain C: N.141, H.144, Y.223, Q.229, C.415, W.420 Ligands: UDP.10 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.141, C:Q.229, C:C.415 Salt bridges: C:H.144 MAN.17: 7 residues within 4Å: Chain D: N.141, H.144, Q.229, C.415, R.416, W.420 Ligands: UDP.15 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.141, D:H.144, D:Q.229, D:R.416 Salt bridges: D:H.144

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 2 residues within 4Å: Chain A: R.58, K.60 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain B: R.58, K.60 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain C: R.58, K.60 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain D: K.60 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Satoh, T. et al., Crystal structure of UDP/mannose-bound AGO61/beta-1,4-N-Acetylglucosaminyltransferase 2 (POMGNT2). To Be Published

Release Date

2024-08-07

Peptides

Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2