SMTL ID : 6giu.1

Human IMPase with L-690330

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

homo-dimer

Ligands

7 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.1: 6 residues within 4Å: Chain A: K.36, D.41, E.70, T.95 Ligands: L69.4, GOL.13 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.70, H2O.3, H2O.5, H2O.6 MN.2: 8 residues within 4Å: Chain A: E.70, D.90, P.91, I.92, D.93, T.95 Ligands: MN.3, L69.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.70, A:D.90, A:I.92, H2O.1 MN.3: 7 residues within 4Å: Chain A: D.90, D.93, G.94, W.219, D.220 Ligands: MN.2, L69.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.90, A:D.93, A:D.220, L69.4 MN.17: 6 residues within 4Å: Chain B: D.90, D.93, W.219, D.220 Ligands: MN.18, L69.21 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.90, B:D.93, B:D.220, L69.21 MN.18: 8 residues within 4Å: Chain B: E.70, D.90, P.91, I.92, D.93, T.95 Ligands: MN.17, L69.21 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.70, B:D.90, B:I.92, H2O.14 MN.19: 5 residues within 4Å: Chain B: K.36, D.41, E.70, T.95 Ligands: L69.21 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.70, H2O.16, H2O.16, H2O.19 MN.20: 2 residues within 4Å: Chain B: D.153, K.156 No protein-ligand interaction detected (PLIP)

2 x L69: [1-(4-oxidanylphenoxy)-1-phosphono-ethyl]phosphonic acid(Non-covalent)

L69.4: 24 residues within 4Å: Chain A: E.70, D.90, I.92, D.93, G.94, T.95, T.96, E.162, G.194, T.195, A.196, N.199, Y.211, E.213, I.216, H.217, W.219, D.220 Ligands: MN.1, MN.2, MN.3, GOL.5, GOL.6, GOL.13 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.196, A:I.216 Hydrogen bonds: A:G.94, A:T.95, A:T.95, A:T.95, A:E.213, A:W.219 Water bridges: A:K.36, A:D.41, A:I.92, A:T.96 L69.21: 24 residues within 4Å: Chain B: E.70, D.90, I.92, D.93, G.94, T.95, T.96, E.162, S.165, G.194, T.195, A.196, Y.211, E.213, I.216, H.217, W.219, D.220 Ligands: GOL.7, MN.17, MN.18, MN.19, GOL.22, GOL.28 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.196, B:I.216 Hydrogen bonds: B:G.94, B:T.95, B:T.95, B:E.213, B:W.219 Water bridges: B:K.36, B:I.92, B:T.96, B:S.165

19 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 13 residues within 4Å: Chain A: E.162, G.164, S.165, E.213, G.215, I.216, H.217, D.220, R.248 Ligands: L69.4, GOL.6, GOL.9, GOL.13 Ligand excluded by PLIP GOL.6: 12 residues within 4Å: Chain A: T.96, E.162, L.163, G.164, S.165, G.194, E.213 Chain B: H.188, G.189, R.191 Ligands: L69.4, GOL.5 Ligand excluded by PLIP GOL.7: 12 residues within 4Å: Chain A: H.188, G.189, R.191 Chain B: T.96, E.162, L.163, G.164, S.165, G.194, E.213 Ligands: L69.21, GOL.22 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: I.154, T.155, I.185, R.261 Ligand excluded by PLIP GOL.9: 11 residues within 4Å: Chain A: S.165, S.166, T.171, M.214, G.215, R.248, I.269, L.271 Ligands: GOL.5, GOL.13, GOL.16 Ligand excluded by PLIP GOL.10: 9 residues within 4Å: Chain A: V.73, E.77, K.78, S.79, I.80, D.274, D.275, E.276, D.277 Ligand excluded by PLIP GOL.11: 13 residues within 4Å: Chain A: T.161, E.162, L.163, M.179, I.190, R.191, S.192 Chain B: T.161, E.162, L.163, M.179, I.190, S.192 Ligand excluded by PLIP GOL.12: 3 residues within 4Å: Chain A: K.36, S.37, A.74 Ligand excluded by PLIP GOL.13: 10 residues within 4Å: Chain A: S.37, D.41, S.165, H.217, R.248 Ligands: MN.1, L69.4, GOL.5, GOL.9, GOL.16 Ligand excluded by PLIP GOL.14: 8 residues within 4Å: Chain A: S.149, Q.151, K.156, H.188, D.209 Chain B: V.99, H.100 Ligands: GOL.15 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain A: S.149, Q.150, Q.151 Chain B: R.101 Ligands: GOL.14 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain A: H.217, R.248, P.270, L.271, Q.272 Ligands: GOL.9, GOL.13 Ligand excluded by PLIP GOL.22: 14 residues within 4Å: Chain B: E.162, G.164, S.165, E.213, M.214, G.215, I.216, H.217, D.220, R.248 Ligands: GOL.7, L69.21, GOL.25, GOL.28 Ligand excluded by PLIP GOL.23: 3 residues within 4Å: Chain B: E.30, M.31, N.32 Ligand excluded by PLIP GOL.24: 8 residues within 4Å: Chain A: M.31, V.33, V.99, H.100 Chain B: Q.151, K.156, H.188, D.209 Ligand excluded by PLIP GOL.25: 10 residues within 4Å: Chain B: S.165, S.166, T.171, M.214, G.215, R.248, I.269, L.271 Ligands: GOL.22, GOL.28 Ligand excluded by PLIP GOL.26: 8 residues within 4Å: Chain B: S.38, P.39, V.40, D.41, S.165, S.166, R.167, T.168 Ligand excluded by PLIP GOL.27: 2 residues within 4Å: Chain B: F.140, G.143 Ligand excluded by PLIP GOL.28: 9 residues within 4Å: Chain B: S.37, D.41, S.165, H.217, W.219, R.248 Ligands: L69.21, GOL.22, GOL.25 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kraft, L. et al., Co-crystallization of human inositol monophosphatase with the lithium mimetic L-690,330. Acta Crystallogr D Struct Biol (2018)

Release Date

2018-10-17

Peptides

Inositol monophosphatase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Inositol monophosphatase 1

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