SMTL ID : 7yq1.1 (2 other biounits)

Crystal structure of adenosine 5'-phosphosulfate kinase from Archaeoglobus fulgidus in complex with AMP-PNP and APS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

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

ADX.1: 19 residues within 4Å: Chain A: S.14, G.41, D.42, R.45, F.54, R.59, H.62, N.63, V.84, V.85, S.86, P.87, K.120, L.122, K.132, G.133, L.134, T.135 Ligands: ANP.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:R.59, A:R.59, A:N.63, A:V.85, A:S.86, A:K.120, A:G.133, A:T.135, A:T.135 Water bridges: A:G.41, A:D.42, A:K.132 Salt bridges: A:R.45, A:R.45, A:R.59, A:H.62 pi-Stacking: A:F.54 ADX.9: 19 residues within 4Å: Chain B: S.14, G.41, D.42, R.45, F.54, R.59, H.62, N.63, V.84, V.85, S.86, P.87, K.120, L.122, K.132, G.133, L.134, T.135 Ligands: ANP.10 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:R.59, B:R.59, B:N.63, B:V.85, B:S.86, B:K.120, B:G.133, B:T.135, B:T.135 Water bridges: B:G.41, B:D.42 Salt bridges: B:R.45, B:R.45, B:R.59, B:H.62 pi-Stacking: B:F.54, B:F.54

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

ANP.2: 22 residues within 4Å: Chain A: P.13, S.14, G.15, A.16, G.17, K.18, T.19, T.20, V.85, R.117, P.119, K.120, L.122, T.153, M.156, T.157, V.158, E.161 Ligands: ADX.1, MG.3, BO3.5, GOL.8 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:G.15, A:A.16, A:G.17, A:K.18, A:K.18, A:T.19, A:T.19, A:T.20, A:T.20, A:T.20, A:K.120, A:M.156 Water bridges: A:T.19, A:D.42, A:R.117, A:T.153 pi-Cation interactions: A:R.117 ANP.10: 20 residues within 4Å: Chain B: P.13, S.14, G.15, A.16, G.17, K.18, T.19, T.20, V.85, R.117, P.119, K.120, L.122, T.153, M.156, V.158, E.161 Ligands: ADX.9, MG.11, BO3.12 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:G.15, B:A.16, B:G.17, B:K.18, B:K.18, B:K.18, B:T.19, B:T.20, B:T.20, B:T.20, B:K.120, B:M.156 Water bridges: B:D.42, B:R.117, B:R.117, B:T.153 pi-Cation interactions: B:R.117

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: T.19, D.40 Ligands: ANP.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.19, H2O.2, H2O.2, H2O.2 MG.11: 3 residues within 4Å: Chain B: T.19, D.40 Ligands: ANP.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.19, H2O.12, H2O.12, H2O.12

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: R.89, A.90, E.93 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.89, A:E.93 Water bridges: A:R.89, A:A.90, A:E.142 GOL.6: 4 residues within 4Å: Chain A: M.115, K.116, R.117, D.118 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.115, A:D.118 GOL.7: 4 residues within 4Å: Chain A: Y.26, K.27, E.30, S.31 No protein-ligand interaction detected (PLIP) GOL.8: 7 residues within 4Å: Chain A: R.117, T.153, D.154, K.155, M.156, T.157 Ligands: ANP.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.117, A:T.153, A:K.155

2 x BO3: BORIC ACID(Non-covalent)

BO3.5: 5 residues within 4Å: Chain A: G.15, D.118, P.119, K.120 Ligands: ANP.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.15, A:D.118, A:D.118, A:K.120 Water bridges: A:S.14, A:D.118, A:K.120 BO3.12: 3 residues within 4Å: Chain B: T.19, T.20 Ligands: ANP.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.20 Water bridges: B:N.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kawakami, T. et al., Crystal structure of adenosine 5'-phosphosulfate kinase isolated from Archaeoglobus fulgidus. Biochem.Biophys.Res.Commun. (2022)

Release Date

2023-01-18

Peptides

Adenylyl-sulfate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Adenylyl-sulfate kinase

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