SMTL ID : 6pky.1 (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- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 8 residues within 4Å: Chain A: E.109, Q.113, T.283, L.284 Chain B: P.60, R.118, L.280, N.281 No protein-ligand interaction detected (PLIP)

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

NAG.2: 4 residues within 4Å: Chain A: R.118, N.281 Chain B: Q.113, T.283 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.118

2 x BR: BROMIDE ION(Non-covalent)

BR.3: 4 residues within 4Å: Chain A: Y.25, A.28, R.29, L.134 Ligand excluded by PLIP BR.12: 5 residues within 4Å: Chain B: Y.25, A.28, R.29, R.127, L.134 Ligand excluded by PLIP

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

CL.4: 1 residues within 4Å: Chain A: K.103 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: F.125, G.135, N.152, S.185 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: N.48 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: Q.244, Q.247, R.248, R.298 Chain B: H.69 Ligand excluded by PLIP CL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: G.71, R.73 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain A: A.116 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: R.64 Chain B: W.297 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain B: G.14 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: R.142, R.143 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain B: V.75, S.76, D.242, G.243, R.248 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain B: S.68, F.258, R.261 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain B: G.71, E.254 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: D.19, D.20, L.21 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
A

B
B

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

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