SMTL ID : 6u11.1

Xenopus laevis N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA) (C46S C219S C453S C480S C486S) with CTD mostly flexible

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 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: 2 residues within 4Å: Chain A: R.38, N.47 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.15: 2 residues within 4Å: Chain B: R.38, N.47 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 10 residues within 4Å: Chain A: M.61, P.62, A.64, T.66, F.125, V.126, I.287, N.288, E.319 Ligands: K.12 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 10 residues within 4Å: Chain B: M.61, P.62, A.64, T.66, F.125, V.126, I.287, N.288, E.319 Ligands: K.26 No protein-ligand interaction detected (PLIP)

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

NAG.3: 3 residues within 4Å: Chain A: N.206, K.209, W.260 No protein-ligand interaction detected (PLIP) NAG.17: 3 residues within 4Å: Chain B: N.206, K.209, W.260 No protein-ligand interaction detected (PLIP)

22 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain A: Y.132, M.135, D.278, S.282, R.309 Ligand excluded by PLIP K.5: 4 residues within 4Å: Chain A: P.42, H.45, Y.204, Q.207 Ligand excluded by PLIP K.6: 4 residues within 4Å: Chain A: R.38, D.39, Q.41, V.43 Ligand excluded by PLIP K.7: 4 residues within 4Å: Chain A: Q.217, T.218, G.220, D.221 Ligand excluded by PLIP K.8: 2 residues within 4Å: Chain A: S.10, T.112 Ligand excluded by PLIP K.9: 3 residues within 4Å: Chain A: K.155, G.156, I.157 Ligand excluded by PLIP K.10: 2 residues within 4Å: Chain A: D.238, E.240 Ligand excluded by PLIP K.11: 6 residues within 4Å: Chain A: Y.301, R.306, C.307 Chain B: T.66, R.67, I.68 Ligand excluded by PLIP K.12: 6 residues within 4Å: Chain A: P.62, A.64, T.65, T.66 Ligands: NAG-NAG.2, NAG-NAG.2 Ligand excluded by PLIP K.13: 6 residues within 4Å: Chain A: D.16, D.17, Q.251, S.296, H.298, R.306 Ligand excluded by PLIP K.14: 3 residues within 4Å: Chain A: V.203, W.260, N.264 Ligand excluded by PLIP K.18: 5 residues within 4Å: Chain B: Y.132, M.135, D.278, S.282, R.309 Ligand excluded by PLIP K.19: 4 residues within 4Å: Chain B: P.42, H.45, Y.204, Q.207 Ligand excluded by PLIP K.20: 4 residues within 4Å: Chain B: R.38, D.39, Q.41, V.43 Ligand excluded by PLIP K.21: 4 residues within 4Å: Chain B: Q.217, T.218, G.220, D.221 Ligand excluded by PLIP K.22: 2 residues within 4Å: Chain B: S.10, T.112 Ligand excluded by PLIP K.23: 3 residues within 4Å: Chain B: K.155, G.156, I.157 Ligand excluded by PLIP K.24: 2 residues within 4Å: Chain B: D.238, E.240 Ligand excluded by PLIP K.25: 6 residues within 4Å: Chain A: T.66, R.67, I.68 Chain B: Y.301, R.306, C.307 Ligand excluded by PLIP K.26: 6 residues within 4Å: Chain B: P.62, A.64, T.65, T.66 Ligands: NAG-NAG.16, NAG-NAG.16 Ligand excluded by PLIP K.27: 6 residues within 4Å: Chain B: D.16, D.17, Q.251, S.296, H.298, R.306 Ligand excluded by PLIP K.28: 3 residues within 4Å: Chain B: V.203, W.260, N.264 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

EGF-like domain-containing protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

EGF-like domain-containing protein