SMTL ID : 6xfi.1

Crystal Structures of beta-1,4-N-Acetylglucosaminyltransferase 2 (POMGNT2): Structural Basis for Inherited Muscular Dystrophies

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

UDP.1: 14 residues within 4Å: Chain A: D.111, N.112, L.113, R.243, T.244, Q.245, N.246, R.247, L.272, E.273, G.295, A.296, Q.297, Y.396 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:N.112, A:L.113, A:T.244, A:Q.245, A:N.246, A:E.273, A:E.273, A:A.296, A:Q.297, A:Q.297 Water bridges: A:R.243, A:R.243, A:R.243, A:N.246, A:L.272, A:Y.396, A:Y.396 Salt bridges: A:R.243, A:R.243, A:R.247, A:R.247 UDP.5: 14 residues within 4Å: Chain B: D.111, N.112, L.113, R.243, T.244, Q.245, N.246, R.247, L.272, E.273, G.295, A.296, Q.297, Y.396 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:N.112, B:L.113, B:T.244, B:Q.245, B:N.246, B:E.273, B:A.296, B:Q.297, B:Q.297, B:Y.396 Water bridges: B:R.243, B:R.243, B:R.243, B:N.246, B:L.272, B:Y.326, B:Y.396 Salt bridges: B:R.243, B:R.243, B:R.247, B:R.247

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

NAG.2: 3 residues within 4Å: Chain A: E.11, N.48 Chain B: R.218 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.48 NAG.6: 3 residues within 4Å: Chain A: R.218 Chain B: E.11, N.48 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.48

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

PO4.3: 6 residues within 4Å: Chain A: P.132, G.133, A.135, H.136 Chain B: R.29, K.31 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Salt bridges: B:R.29, B:K.31, A:H.136 Hydrogen bonds: A:G.133 Water bridges: A:A.135, A:A.135 PO4.4: 8 residues within 4Å: Chain A: R.214, L.302, L.304, P.305, R.306, G.334, M.335, L.337 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.335 Water bridges: A:R.306 Salt bridges: A:R.214 PO4.7: 6 residues within 4Å: Chain A: R.29, K.31 Chain B: P.132, G.133, A.135, H.136 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Salt bridges: A:R.29, A:K.31, B:H.136 Hydrogen bonds: B:G.133 Water bridges: B:A.135, B:A.135 PO4.8: 8 residues within 4Å: Chain B: R.214, L.302, L.304, P.305, R.306, G.334, M.335, L.337 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.335 Water bridges: B:R.306 Salt bridges: B:R.214

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

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