SMTL ID : 2q7d.3 (3 other biounits)

Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-kinase (ITPK1) in complex with AMPPNP and Mn2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 3 residues within 4Å: Chain A: D.306, N.308 Ligands: ANP.10 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.306, A:D.306, H2O.4, H2O.5 MN.2: 4 residues within 4Å: Chain A: K.210, D.292, D.306 Ligands: ANP.10 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.292, A:D.306, H2O.3 MN.11: 4 residues within 4Å: Chain B: K.210, D.292, D.306 Ligands: ANP.18 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.292, B:D.306, H2O.19 MN.12: 3 residues within 4Å: Chain B: D.306, N.308 Ligands: ANP.18 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.306, B:D.306, H2O.20, H2O.24

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

SO4.3: 8 residues within 4Å: Chain A: G.174, T.175, N.176, S.177, H.178, E.179, N.242, H.244 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.176, A:S.177, A:H.178, A:E.179, A:N.242 Water bridges: A:E.179, A:E.179 Salt bridges: A:H.178 SO4.4: 8 residues within 4Å: Chain A: K.210, F.212, R.223, K.248, P.311, G.312, Y.313, E.314 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.312, A:Y.313, A:E.314 Water bridges: A:K.210, A:R.223, A:K.248, A:E.314, A:E.314 Salt bridges: A:K.210, A:R.223, A:K.248 SO4.5: 4 residues within 4Å: Chain A: T.169, R.170, V.171, P.195 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.170, A:V.171 Water bridges: A:R.170 Salt bridges: A:R.170 SO4.6: 4 residues within 4Å: Chain A: K.227, F.229, R.236, D.259 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.236, A:R.236 Salt bridges: A:K.227, A:R.236 SO4.7: 3 residues within 4Å: Chain A: H.8, H.9, H.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.9, A:H.10 Salt bridges: A:H.8 SO4.8: 4 residues within 4Å: Chain A: K.4, I.5, H.6, H.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.6, A:H.7 Water bridges: A:K.4, A:H.6 Salt bridges: A:H.7 SO4.9: 3 residues within 4Å: Chain A: S.269, D.270, E.271 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.269, A:D.270, A:E.271 Water bridges: A:R.274 SO4.13: 4 residues within 4Å: Chain A: R.274, R.278 Chain B: R.274, R.278 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Water bridges: B:E.271, B:R.274, B:R.278, B:R.278, B:R.278, A:R.278, A:R.278 Salt bridges: B:R.274, B:R.278, A:R.274, A:R.278 SO4.14: 3 residues within 4Å: Chain B: S.269, D.270, E.271 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.270, B:D.270, B:E.271 Water bridges: B:R.274, B:R.274 SO4.15: 4 residues within 4Å: Chain B: K.29, K.70, H.173, F.310 5 PLIP interactions: 5 interactions with chain B Water bridges: B:K.70 Salt bridges: B:K.28, B:K.29, B:K.70, B:H.173 SO4.16: 8 residues within 4Å: Chain B: K.210, F.212, R.223, K.248, P.311, G.312, Y.313, E.314 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.312, B:Y.313, B:E.314 Water bridges: B:K.32, B:K.210, B:K.210, B:R.223, B:R.223 Salt bridges: B:K.210, B:R.223, B:K.248 SO4.17: 3 residues within 4Å: Chain B: H.6, H.7, H.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.7, B:H.8 Salt bridges: B:H.6, B:H.8

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.10: 24 residues within 4Å: Chain A: R.117, I.166, K.168, H.178, M.180, Q.199, N.200, F.201, I.202, H.204, L.208, K.210, S.225, L.226, S.243, V.246, S.247, D.292, I.294, I.305, D.306, N.308 Ligands: MN.1, MN.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:R.117, A:K.168, A:Q.199, A:I.202, A:K.210, A:L.226, A:S.243, A:S.247, A:S.247 Water bridges: A:H.178, A:S.243, A:S.243, A:S.247, A:K.248, A:K.248, A:N.308 Salt bridges: A:K.168 ANP.18: 26 residues within 4Å: Chain B: R.117, I.166, K.168, H.178, M.180, Q.199, N.200, F.201, I.202, H.204, L.208, K.210, S.225, L.226, F.241, S.243, H.244, V.246, S.247, D.292, I.294, I.305, D.306, N.308 Ligands: MN.11, MN.12 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:R.117, B:Y.121, B:K.168, B:Q.199, B:I.202, B:K.210, B:L.226, B:S.243, B:S.243, B:S.247, B:S.247, B:D.292, B:D.306, B:N.308 Water bridges: B:R.117, B:A.172, B:A.172, B:H.244, B:S.247, B:D.292, B:D.306, B:N.308, B:N.308 Salt bridges: B:K.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chamberlain, P.P. et al., Integration of inositol phosphate signaling pathways via human ITPK1. J.Biol.Chem. (2007)

Release Date

2007-07-03

Peptides

Inositol-tetrakisphosphate 1-kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Inositol-tetrakisphosphate 1-kinase

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