SMTL ID : 8i1m.1

Crystal structure of oxidated APSK1 domain from human PAPSS1 in complex with APS and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 11 residues within 4Å: Chain A: G.38, G.40, T.43, V.44, R.144, T.180, D.181, C.183, D.184, V.185, C.188 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.40, A:T.43 Water bridges: A:G.38 Salt bridges: A:R.144 ADP.4: 11 residues within 4Å: Chain B: G.38, G.40, T.43, V.44, R.144, T.180, D.181, C.183, D.184, V.185, C.188 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.40, B:D.181 Water bridges: B:G.38 Salt bridges: B:R.144

2 x ADX: ADENOSINE-5'-PHOSPHOSULFATE(Non-covalent)

ADX.2: 14 residues within 4Å: Chain A: R.68, F.77, R.82, N.85, F.107, I.108, S.109, P.110, L.149, I.158, K.159, G.160, F.161, T.162 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.82, A:R.82, A:N.85, A:I.108, A:S.109, A:G.160, A:T.162, A:T.162 Water bridges: A:S.37 Salt bridges: A:R.68, A:R.68, A:R.82 pi-Stacking: A:F.77, A:F.77 ADX.5: 14 residues within 4Å: Chain B: R.68, F.77, R.82, N.85, F.107, I.108, S.109, P.110, L.149, I.158, K.159, G.160, F.161, T.162 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:R.82, B:R.82, B:N.85, B:I.108, B:S.109, B:G.160, B:T.162 Water bridges: B:S.37 Salt bridges: B:R.68, B:R.68, B:R.82 pi-Stacking: B:F.77, B:F.77

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

PO4.3: 8 residues within 4Å: Chain A: T.112, R.115, N.116, E.131, P.171, E.172, A.173, P.174 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.116, A:E.172, A:A.173 Water bridges: A:R.115, A:N.116, A:N.116, A:R.119, A:E.131 Salt bridges: A:R.115 PO4.6: 8 residues within 4Å: Chain B: T.112, R.115, N.116, E.131, P.171, E.172, A.173, P.174 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.116, B:E.172, B:A.173 Water bridges: B:R.115, B:N.116, B:N.116, B:R.119, B:E.131 Salt bridges: B:R.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, L. et al., Redox switching mechanism of the adenosine 5'-phosphosulfate kinase domain (APSK2) of human PAPS synthase 2. Structure (2023)

Release Date

2023-06-28

Peptides

PAPSS1 protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PAPSS1 protein