SMTL ID : 7yq0.1

Crystal structure of adenosine 5'-phosphosulfate kinase from Archaeoglobus fulgidus in complex with ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 16 residues within 4Å: Chain A: P.13, S.14, G.15, A.16, G.17, K.18, T.19, T.20, R.117, T.153, M.156, T.157, V.158, E.161 Ligands: GOL.4, GOL.6 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:G.15, A:A.16, A:G.17, A:K.18, A:T.19, A:T.19, A:T.20, A:T.20, A:R.117, A:M.156 Water bridges: A:S.14, A:K.18, A:R.117 Salt bridges: A:K.18 pi-Cation interactions: A:R.117 ADP.7: 14 residues within 4Å: Chain B: P.13, S.14, G.15, A.16, G.17, K.18, T.19, T.20, R.117, T.153, M.156, T.157, V.158, E.161 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:P.13, B:G.15, B:A.16, B:G.17, B:K.18, B:T.19, B:T.20, B:T.20, B:M.156 Water bridges: B:S.14, B:K.18, B:T.20, B:R.117, B:R.117, B:R.117, B:T.153, B:V.158 Salt bridges: B:K.18 pi-Cation interactions: B:R.117

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: R.96, F.102, E.148, Y.174 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.96, A:R.96, A:F.102, A:E.148, A:Y.174, A:Y.174 GOL.3: 3 residues within 4Å: Chain A: R.108, C.109, P.110 7 PLIP interactions: 7 interactions with chain A Water bridges: A:Y.106, A:C.109, A:L.111, A:L.111, A:D.138, A:D.152, A:D.154 GOL.4: 8 residues within 4Å: Chain A: K.18, T.19, D.40, G.41, D.42, S.83, V.85 Ligands: ADP.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.18, A:K.18, A:T.19, A:T.19, A:D.40, A:D.42 Water bridges: A:V.85 GOL.5: 6 residues within 4Å: Chain A: S.5, F.6, Y.34, I.79, Y.174, L.175 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.5, A:Y.174 Water bridges: A:R.35 GOL.6: 7 residues within 4Å: Chain A: R.117, T.153, D.154, K.155, M.156, T.157 Ligands: ADP.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.117, A:T.153 Water bridges: A:T.157, A:V.158 GOL.8: 9 residues within 4Å: Chain B: M.4, S.5, F.6, Y.34, G.77, I.79, K.101, Y.174, L.175 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.77, B:K.101, B:K.101, B:L.175 Water bridges: B:Y.34, B:I.79, B:L.175 GOL.9: 6 residues within 4Å: Chain A: Y.49, N.51, L.52 Chain B: E.57, E.58, M.61 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.51, A:N.51 Water bridges: A:N.51, A:L.52, B:E.57 GOL.10: 3 residues within 4Å: Chain B: E.56, Y.88, W.91 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.56

1 x NA: SODIUM ION(Non-functional Binders)

NA.11: 3 residues within 4Å: Chain B: R.96, I.99, E.100 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.100

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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