SMTL ID : 6zk0.1

1.47A human IMPase with ebselen

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 6 residues within 4Å: Chain A: K.38, L.44, E.72, E.73 Ligands: MN.2, MN.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.38, A:K.38 Water bridges: A:T.97 NA.4: 5 residues within 4Å: Chain A: D.92, D.95, D.222 Ligands: MN.3, GOL.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.95 NA.13: 2 residues within 4Å: Chain A: H.102 Chain B: D.211 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.211, A:H.102 NA.14: 1 residues within 4Å: Chain A: E.267 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.267, A:E.267 NA.15: 3 residues within 4Å: Chain A: G.196 Ligands: SO4.5, GOL.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.196 Water bridges: A:T.98 NA.16: 3 residues within 4Å: Chain A: G.208, D.211 Chain B: H.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.211 NA.17: 6 residues within 4Å: Chain B: D.92, D.95, D.222 Ligands: MN.18, MN.19, GOL.22 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.222 NA.28: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

6 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 6 residues within 4Å: Chain A: K.38, L.44, E.72 Ligands: NA.1, MN.3, SO4.5 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.72, H2O.1, H2O.1, H2O.2, H2O.2 MN.3: 9 residues within 4Å: Chain A: E.72, D.92, I.94, D.95, T.97 Ligands: NA.1, MN.2, NA.4, SO4.5 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.72, A:D.92, A:I.94, H2O.2, H2O.2, H2O.3 MN.18: 7 residues within 4Å: Chain B: D.92, D.95, D.222 Ligands: NA.17, MN.19, GOL.22, SO4.23 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.92, B:D.95, B:D.222, H2O.13, H2O.14 MN.19: 9 residues within 4Å: Chain B: E.72, D.92, I.94, D.95, T.97 Ligands: NA.17, MN.18, MN.20, MN.21 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.72, B:D.92, B:I.94, H2O.9, H2O.12, H2O.14 MN.20: 7 residues within 4Å: Chain B: K.38, D.43, L.44, E.72 Ligands: MN.19, MN.21, SO4.23 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.72, H2O.9, H2O.10, H2O.10, H2O.10 MN.21: 4 residues within 4Å: Chain B: E.72 Ligands: MN.19, MN.20, SO4.23 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.72, H2O.9, H2O.10, H2O.10, H2O.14

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 10 residues within 4Å: Chain A: I.94, D.95, G.96, T.97, T.98, G.196 Ligands: MN.2, MN.3, GOL.9, NA.15 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.96, A:T.97, A:T.98, A:T.98, A:T.98 Water bridges: A:D.43, A:T.97, A:N.99 SO4.23: 9 residues within 4Å: Chain B: I.94, D.95, G.96, T.97, T.98 Ligands: MN.18, MN.20, MN.21, GOL.22 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.96, B:T.97, B:T.97, B:T.98 Water bridges: B:D.43, B:L.44, B:L.44, B:T.98, B:N.99

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: I.156, T.157, R.263 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.263, A:R.263 GOL.7: 4 residues within 4Å: Chain A: R.250, L.273, Q.274 Ligands: GOL.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.250, A:R.250, A:Q.274 GOL.8: 7 residues within 4Å: Chain A: L.165, I.192, R.193, S.194 Chain B: I.192, R.193, S.194 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.165, A:I.192, A:S.194, B:S.194, B:S.194 GOL.9: 9 residues within 4Å: Chain A: D.95, E.164, T.197, A.198, E.215, D.222 Ligands: NA.4, SO4.5, NA.15 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.95, A:A.198, A:E.215, A:D.222 Water bridges: A:H.219 GOL.10: 2 residues within 4Å: Chain A: F.142, G.145 No protein-ligand interaction detected (PLIP) GOL.11: 6 residues within 4Å: Chain A: D.43, S.167, G.217, H.219, R.250 Ligands: GOL.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.167, A:G.217 Water bridges: A:D.43 GOL.22: 9 residues within 4Å: Chain B: D.95, E.164, T.197, A.198, E.215, D.222 Ligands: NA.17, MN.18, SO4.23 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.198, B:E.215 GOL.24: 3 residues within 4Å: Chain B: R.250, L.273, Q.274 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.250, B:R.250, B:Q.274 Water bridges: B:H.219 GOL.26: 2 residues within 4Å: Chain B: E.27, N.31 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.27, B:E.27, B:N.31

2 x 9JT: N-phenyl-2-selanylbenzamide(Non-covalent)

9JT.12: 5 residues within 4Å: Chain A: K.131, C.143, N.144, Q.146, T.207 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.144, A:T.207 Hydrogen bonds: A:Q.146 Water bridges: A:N.144 9JT.27: 5 residues within 4Å: Chain B: K.131, C.143, N.144, Q.146, T.207 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:N.144, B:T.207 Hydrogen bonds: B:Q.146 Water bridges: B:N.144

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.25: 5 residues within 4Å: Chain B: A.265, K.266, E.267, I.268, Q.269 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fenn, G.D. et al., Crystallization and structure of ebselen bound to Cys141 of human inositol monophosphatase. Acta Crystallogr.,Sect.F (2020)

Release Date

2020-09-23

Peptides

Inositol monophosphatase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

Inositol monophosphatase 1