SMTL ID : 5tcd.1

Human alkaline sphingomyelinase (ENPP7) in complex with phosphocholine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

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.1: 7 residues within 4Å: Chain A: Y.87, N.89, T.91, S.92, R.106 Ligands: NAG-NAG.2, IOD.35 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 7 residues within 4Å: Chain A: D.109, N.110, G.111, P.314, R.315 Ligands: NAG-NAG.1, IOD.35 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 11 residues within 4Å: Chain A: N.135, V.136, T.137, A.142, S.146, R.147, K.148 Ligands: IOD.16, IOD.22, IOD.25, IOD.36 No protein-ligand interaction detected (PLIP)

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.4: 8 residues within 4Å: Chain A: R.147, N.154, N.157, T.159, E.160, A.163, N.164 Ligands: IOD.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.160, A:A.163

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 8 residues within 4Å: Chain A: D.28, G.29, T.64, H.68, D.235, H.236, H.342 Ligands: PC.46 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.28, A:D.28, A:T.64, A:D.235, A:H.236 ZN.6: 6 residues within 4Å: Chain A: D.188, H.192, H.236, M.238, H.342 Ligands: PC.46 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.188, A:D.188, A:H.192, A:H.342

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

NAG.7: 3 residues within 4Å: Chain A: P.255, N.256 Ligands: IOD.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.256

1 x NA: SODIUM ION(Non-functional Binders)

NA.8: 4 residues within 4Å: Chain A: D.35, V.38, D.39, T.40 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.35, A:T.40

37 x IOD: IODIDE ION(Non-functional Binders)

IOD.9: 4 residues within 4Å: Chain A: T.57, P.370, F.371, E.372 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain A: N.154, K.156, N.157 Ligands: NAG-NAG-FUC.4 Ligand excluded by PLIP IOD.11: 4 residues within 4Å: Chain A: K.93, K.95, F.264, E.265 Ligand excluded by PLIP IOD.12: 5 residues within 4Å: Chain A: K.156, S.189, T.190, R.193, Y.194 Ligand excluded by PLIP IOD.13: 5 residues within 4Å: Chain A: Y.87, N.89, S.92, V.94, R.106 Ligand excluded by PLIP IOD.14: 6 residues within 4Å: Chain A: F.254, P.255, N.256, A.288, A.292 Ligands: NAG.7 Ligand excluded by PLIP IOD.15: 4 residues within 4Å: Chain A: K.301, N.312, N.313, P.314 Ligand excluded by PLIP IOD.16: 4 residues within 4Å: Chain A: Q.105, V.136, T.137 Ligands: NAG-NAG-BMA.3 Ligand excluded by PLIP IOD.17: 1 residues within 4Å: Chain A: K.93 Ligand excluded by PLIP IOD.18: 4 residues within 4Å: Chain A: S.361, R.382, L.383, L.402 Ligand excluded by PLIP IOD.19: 3 residues within 4Å: Chain A: E.158, T.159, R.162 Ligand excluded by PLIP IOD.20: 4 residues within 4Å: Chain A: T.90, L.276, T.317, P.318 Ligand excluded by PLIP IOD.21: 1 residues within 4Å: Chain A: T.240 Ligand excluded by PLIP IOD.22: 3 residues within 4Å: Chain A: R.145 Ligands: NAG-NAG-BMA.3, NAG-NAG-BMA.3 Ligand excluded by PLIP IOD.23: 2 residues within 4Å: Chain A: T.91, S.92 Ligand excluded by PLIP IOD.24: 3 residues within 4Å: Chain A: P.199, E.200, E.203 Ligand excluded by PLIP IOD.25: 4 residues within 4Å: Chain A: S.146, R.147, W.171 Ligands: NAG-NAG-BMA.3 Ligand excluded by PLIP IOD.26: 4 residues within 4Å: Chain A: Y.98, H.99, Y.155 Ligands: PC.46 Ligand excluded by PLIP IOD.27: 2 residues within 4Å: Chain A: R.125, R.145 Ligand excluded by PLIP IOD.28: 4 residues within 4Å: Chain A: L.276, P.277, L.282, P.318 Ligand excluded by PLIP IOD.29: 4 residues within 4Å: Chain A: K.21, T.173, L.224, R.227 Ligand excluded by PLIP IOD.30: 4 residues within 4Å: Chain A: Y.194, G.195, T.240, N.339 Ligand excluded by PLIP IOD.31: 3 residues within 4Å: Chain A: R.363, A.364, H.403 Ligand excluded by PLIP IOD.32: 2 residues within 4Å: Chain A: K.253, P.255 Ligand excluded by PLIP IOD.33: 4 residues within 4Å: Chain A: N.154, Y.155, K.156, S.189 Ligand excluded by PLIP IOD.34: 4 residues within 4Å: Chain A: M.63, Y.269, H.342, G.343 Ligand excluded by PLIP IOD.35: 3 residues within 4Å: Ligands: NAG-NAG.1, NAG-NAG.2, NAG-NAG.2 Ligand excluded by PLIP IOD.36: 3 residues within 4Å: Chain A: R.147 Ligands: NAG-NAG-BMA.3, NAG-NAG-BMA.3 Ligand excluded by PLIP IOD.37: 2 residues within 4Å: Chain A: P.97, A.100 Ligand excluded by PLIP IOD.38: 2 residues within 4Å: Chain A: V.368, P.400 Ligand excluded by PLIP IOD.39: 2 residues within 4Å: Chain A: A.396, T.397 Ligand excluded by PLIP IOD.40: 4 residues within 4Å: Chain A: G.103, I.104, Q.105, R.106 Ligand excluded by PLIP IOD.41: 4 residues within 4Å: Chain A: H.99, K.148, E.149, G.150 Ligand excluded by PLIP IOD.42: 2 residues within 4Å: Chain A: K.75, N.79 Ligand excluded by PLIP IOD.43: 2 residues within 4Å: Chain A: Y.214, E.217 Ligand excluded by PLIP IOD.44: 4 residues within 4Å: Chain A: G.150, I.151, A.152 Ligands: IOD.45 Ligand excluded by PLIP IOD.45: 4 residues within 4Å: Chain A: G.150, A.152, H.153 Ligands: IOD.44 Ligand excluded by PLIP

1 x PC: PHOSPHOCHOLINE(Non-covalent)

PC.46: 15 residues within 4Å: Chain A: D.28, T.64, N.85, Y.98, Y.155, Y.183, G.185, D.188, S.189, H.192, Y.269, H.342 Ligands: ZN.5, ZN.6, IOD.26 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.64, A:N.85, A:Y.269 Salt bridges: A:D.28, A:D.188, A:H.192, A:H.342 pi-Cation interactions: A:Y.155

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorelik, A. et al., Crystal structure of the human alkaline sphingomyelinase provides insights into substrate recognition. J. Biol. Chem. (2017)

Release Date

2017-03-22

Peptides

Ectonucleotide pyrophosphatase/phosphodiesterase family member 7: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ectonucleotide pyrophosphatase/phosphodiesterase family member 7

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