SMTL ID : 6pky.2 (1 other biounit)

Guinea pig N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA) catalytic domain auto-inhibited by pro-peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 7 residues within 4Å: Chain A: V.63, R.118, L.280, N.281 Chain B: Q.113, T.283 Ligands: CL.5 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.281

2 x BR: BROMIDE ION(Non-covalent)

BR.2: 4 residues within 4Å: Chain A: A.28, R.29, R.127, L.134 Ligand excluded by PLIP BR.10: 4 residues within 4Å: Chain B: Y.25, A.28, R.29, L.134 Ligand excluded by PLIP

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

CL.3: 1 residues within 4Å: Chain A: N.129 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: G.95, G.96, P.97, R.104 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: R.118 Ligands: NAG.1 Ligand excluded by PLIP CL.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: K.217, V.221, T.245 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: V.23, P.26, S.214 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: R.81, D.233 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain B: Q.102 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain B: T.176 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: R.105, R.302 Ligand excluded by PLIP CL.14: 7 residues within 4Å: Chain B: Y.25, R.29, R.31, F.125, L.134, N.152, V.187 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain B: R.17 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain B: F.125, F.126, M.128, D.271 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain B: R.29, Q.151, N.152, T.204, E.205 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain B: R.118 Ligand excluded by PLIP CL.19: 1 residues within 4Å: Chain B: D.160 Ligand excluded by PLIP CL.20: 1 residues within 4Å: Chain B: E.257 Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain B: K.45 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 (NAGPA): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA)

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