SMTL ID : 6xi2.1 (1 other biounit)

Apo form of POMGNT2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 9 residues within 4Å: Chain A: V.230, S.231, A.232, T.233, G.234, V.235, R.286, S.289, N.290 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.231, A:G.234 NAG.10: 3 residues within 4Å: Chain B: S.453, N.491, T.493 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.491

14 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: N.116, R.247, R.251, G.299, A.300 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.116, A:N.116, A:R.247, A:A.300 Water bridges: A:Y.400 Salt bridges: A:R.251 PO4.3: 4 residues within 4Å: Chain A: R.143, P.164, K.165, Q.166 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.164, A:Q.166 Salt bridges: A:R.143 PO4.4: 3 residues within 4Å: Chain A: V.100, G.177, R.178 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.178 Salt bridges: A:R.178 PO4.5: 6 residues within 4Å: Chain A: R.33, K.35 Chain B: P.132, G.133, A.135, H.136 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.33, A:K.35 Hydrogen bonds: B:G.133 PO4.6: 3 residues within 4Å: Chain A: R.133, H.140, F.223 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.133, A:H.140 PO4.7: 2 residues within 4Å: Chain A: G.420, R.421 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.421 PO4.8: 2 residues within 4Å: Chain A: R.439, K.466 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.439, A:K.466 PO4.9: 2 residues within 4Å: Chain A: R.222, R.310 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.218, A:R.310 Salt bridges: A:R.222, A:R.310 PO4.11: 6 residues within 4Å: Chain A: P.136, G.137, A.139, H.140 Chain B: R.29, K.31 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.137, A:H.140 Water bridges: A:A.139, B:R.29 Salt bridges: B:R.29, B:K.31 PO4.12: 2 residues within 4Å: Chain B: R.434, K.461 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.434, B:K.461 PO4.13: 3 residues within 4Å: Chain B: V.96, G.173, R.174 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.174 Salt bridges: B:R.174 PO4.14: 3 residues within 4Å: Chain B: K.203, A.204, N.205 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.204, B:N.205, B:N.205, B:N.205 PO4.15: 5 residues within 4Å: Chain B: N.112, R.243, R.247, G.295, A.296 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.112, B:N.112, B:A.296 Salt bridges: B:R.243, B:R.247 PO4.16: 4 residues within 4Å: Chain B: Q.376, S.377, R.378, E.379 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.376, B:R.378, B:E.379 Salt bridges: B:R.378

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, J.Y. et al., Crystal structures of beta-1,4-N-acetylglucosaminyltransferase 2: structural basis for inherited muscular dystrophies. Acta Crystallogr D Struct Biol (2021)

Release Date

2021-04-21

Peptides

Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2: A
Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2: B
ALA-GLY-ALA-GLY-ALA-ALA-ALA-ALA-ALA-ALA: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
H

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

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

ALA-GLY-ALA-GLY-ALA-ALA-ALA-ALA-ALA-ALA