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

Zebrafish N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA) catalytic domain (C56S C230S) in complex with N-acetyl-alpha-D-glucosamine (alpha-GlcNAc) and mannose 6-phosphate (M6P)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: I.193, N.196, R.213, W.250 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.196, A:R.213, A:R.213 NAG.2: 5 residues within 4Å: Chain A: L.115, N.278 Chain B: K.110, N.278 Ligands: NAG.8 5 PLIP interactions: 5 interactions with chain A Water bridges: A:N.278, A:N.278, A:N.278, A:N.278, A:S.280 NAG.7: 4 residues within 4Å: Chain B: I.193, N.196, R.213, W.250 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.250 Hydrogen bonds: B:N.196 Water bridges: B:N.196 NAG.8: 8 residues within 4Å: Chain A: K.110 Chain B: L.53, S.55, L.115, V.116, L.277, N.278 Ligands: NAG.2 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.277 Hydrogen bonds: B:N.278 Water bridges: A:K.110, A:K.110

2 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)

NDG.3: 16 residues within 4Å: Chain A: S.10, G.11, P.12, Y.122, F.123, T.125, F.215, S.220, R.222, D.268, G.269, G.270, G.271, S.272, R.298 Ligands: M6P.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.10, A:S.10, A:S.10, A:F.123, A:F.123, A:G.269 Water bridges: A:S.10, A:R.222 Salt bridges: A:R.298 NDG.9: 16 residues within 4Å: Chain B: S.10, G.11, P.12, Y.122, F.123, T.125, F.215, S.220, R.222, D.268, G.269, G.270, G.271, S.272, R.298 Ligands: M6P.10 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.10, B:S.10, B:S.10, B:F.123, B:F.123, B:G.269 Water bridges: B:S.10 Salt bridges: B:R.298

2 x M6P: 6-O-phosphono-alpha-D-mannopyranose(Non-covalent)

M6P.4: 9 residues within 4Å: Chain A: G.9, S.10, S.220, T.242, G.270, G.271, S.286, R.298 Ligands: NDG.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.10, A:S.10, A:T.242, A:G.271 Water bridges: A:S.10, A:S.10, A:T.242, A:T.242, A:S.286, A:D.287 Salt bridges: A:R.298 M6P.10: 8 residues within 4Å: Chain B: G.9, S.10, T.242, G.270, G.271, S.286, R.298 Ligands: NDG.9 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.10, B:T.242, B:G.271 Water bridges: B:S.10, B:S.10, B:T.242, B:T.242, B:R.298, B:R.298 Salt bridges: B:R.298

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.5: 10 residues within 4Å: Chain A: S.20, H.21, S.22, H.23, R.24, G.145, G.146, I.147, Q.148, S.166 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.23, A:R.24 Water bridges: A:R.24

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

CL.6: 1 residues within 4Å: Chain A: R.24 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: S.22, Y.25 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: H.214, D.217, V.218 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorelik, A. et al., Crystal Structure of the Mannose-6-Phosphate Uncovering Enzyme. Structure (2020)

Release Date

2020-02-19

Peptides

N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase

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