SMTL ID : 2ofx.1

crystal structure of the APSK domain of human PAPSS1 in complex with ADPMg and PAPS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: T.46, D.67, D.69 Ligands: PPS.4, ADP.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.46, H2O.2, H2O.3, H2O.3 MG.6: 5 residues within 4Å: Chain B: T.46, D.67, D.69 Ligands: PPS.9, ADP.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.46, H2O.4, H2O.6, H2O.6

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 8 residues within 4Å: Chain A: T.116, R.119, N.120, E.135, P.175, E.176, A.177, P.178 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.120, A:N.120, A:E.135, A:E.176, A:A.177 Water bridges: A:T.116, A:R.119 Salt bridges: A:R.119 PO4.3: 2 residues within 4Å: Chain A: P.141, H.143 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.143 PO4.7: 7 residues within 4Å: Chain B: R.119, N.120, E.135, P.175, E.176, A.177, P.178 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.120, B:E.135, B:E.176, B:A.177 Water bridges: B:T.116, B:R.119 Salt bridges: B:R.119 PO4.8: 2 residues within 4Å: Chain B: P.141, H.143 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.143

2 x PPS: 3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE(Non-covalent)

PPS.4: 27 residues within 4Å: Chain A: S.41, G.42, K.45, T.46, G.68, D.69, R.72, F.81, R.86, N.89, V.90, F.111, I.112, S.113, P.114, K.151, L.153, I.162, K.163, G.164, F.165, T.166 Chain B: T.6, N.7, V.8 Ligands: MG.1, ADP.5 26 PLIP interactions: 25 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.41, A:S.41, A:G.42, A:D.69, A:R.86, A:R.86, A:N.89, A:I.112, A:S.113, A:G.164, A:T.166, B:N.7 Water bridges: A:T.46, A:D.69, A:D.69, A:D.69, A:K.151, A:K.151, A:K.151 Salt bridges: A:K.45, A:R.72, A:R.72, A:R.86, A:K.151 pi-Stacking: A:F.81, A:F.81 PPS.9: 25 residues within 4Å: Chain A: T.6, N.7, V.8 Chain B: S.41, G.42, K.45, G.68, D.69, R.72, F.81, R.86, N.89, V.90, F.111, I.112, S.113, P.114, K.151, L.153, K.163, G.164, F.165, T.166 Ligands: MG.6, ADP.10 26 PLIP interactions: 25 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.41, B:S.41, B:G.42, B:R.86, B:R.86, B:N.89, B:I.112, B:S.113, B:G.164, B:T.166, B:T.166, A:N.7 Water bridges: B:T.46, B:D.69, B:D.69, B:D.69, B:K.151, B:K.151, B:K.151 Salt bridges: B:K.45, B:R.72, B:R.72, B:R.86, B:K.151 pi-Stacking: B:F.81, B:F.81

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.5: 16 residues within 4Å: Chain A: L.40, S.41, G.42, A.43, G.44, K.45, T.46, T.47, R.148, V.150, T.184, C.187, D.188, V.189 Ligands: MG.1, PPS.4 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.41, A:G.42, A:A.43, A:G.44, A:K.45, A:T.46, A:T.47, A:T.47, A:R.148, A:C.187 Water bridges: A:T.46, A:K.151 Salt bridges: A:K.45 pi-Cation interactions: A:R.148, A:R.148 ADP.10: 17 residues within 4Å: Chain B: L.40, S.41, G.42, A.43, G.44, K.45, T.46, T.47, R.148, V.150, T.184, C.187, D.188, V.189, C.192 Ligands: MG.6, PPS.9 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.42, B:A.43, B:G.44, B:K.45, B:T.46, B:T.46, B:T.47, B:T.47, B:R.148, B:R.148, B:C.187 Water bridges: B:K.151, A:Q.11 Salt bridges: B:K.45, B:K.151 pi-Cation interactions: B:R.148, B:R.148

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sekulic, N. et al., Elucidation of the Active Conformation of the APS-Kinase Domain of Human PAPS Synthetase 1. J.Mol.Biol. (2007)

Release Date

2007-04-10

Peptides

Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1