SMTL ID : 1m7g.5 (4 other biounits)

Crystal structure of APS kinase from Penicillium Chrysogenum: Ternary structure with ADP and APS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: L.12, T.13, R.14, R.17 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.14 Water bridges: A:R.17, A:R.17 Salt bridges: A:R.17 SO4.2: 5 residues within 4Å: Chain A: R.14, R.17, R.21, T.202, K.203 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:R.14, A:R.17, A:R.21, A:K.203 SO4.3: 8 residues within 4Å: Chain A: R.110, R.113, D.114, E.135, P.175, A.176, N.177, P.178 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.135, A:A.176, A:N.177 Water bridges: A:R.117, A:R.117, A:R.117 Salt bridges: A:R.110, A:R.113 SO4.6: 8 residues within 4Å: Chain B: R.110, R.113, D.114, E.135, P.175, A.176, N.177, P.178 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.110, B:D.114, B:A.176, B:N.177 Water bridges: B:R.117, B:R.117 Salt bridges: B:R.113 SO4.10: 5 residues within 4Å: Chain C: R.14, R.17, R.21, T.202, K.203 4 PLIP interactions: 4 interactions with chain C Salt bridges: C:R.14, C:R.17, C:R.21, C:K.203 SO4.11: 6 residues within 4Å: Chain C: R.110, R.113, E.135, P.175, A.176, N.177 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.135, C:A.176, C:N.177 Water bridges: C:R.117, C:R.117 Salt bridges: C:R.113

2 x AV2: ADENOSINE-5'-DIPHOSPHATE-2',3'-VANADATE(Non-covalent)

AV2.4: 16 residues within 4Å: Chain A: L.33, S.34, A.35, S.36, G.37, K.38, S.39, T.40, R.148, N.184, L.187, V.189 Chain C: R.148, D.149, P.150 Ligands: AV2.12 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:A.35, A:S.36, A:G.37, A:K.38, A:S.39, A:T.40, A:T.40, A:R.148, A:N.184, A:L.187 Water bridges: A:K.38, A:K.38, A:E.186, A:L.187, C:D.149 Salt bridges: A:K.38 pi-Cation interactions: A:R.148, A:R.148 AV2.12: 16 residues within 4Å: Chain A: R.148, D.149, P.150 Chain C: L.33, S.34, A.35, S.36, G.37, K.38, S.39, T.40, R.148, N.184, L.187, V.189 Ligands: AV2.4 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:A.35, C:S.36, C:G.37, C:K.38, C:S.39, C:T.40, C:T.40, C:R.148, C:N.184, C:L.187 Water bridges: C:K.38, C:K.38, C:R.148, C:E.186, C:E.186, A:D.149 Salt bridges: C:K.38 pi-Cation interactions: C:R.148, C:R.148

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

ADX.5: 16 residues within 4Å: Chain A: S.34, R.66, F.75, R.80, N.83, I.84, F.105, I.106, S.107, P.108, L.153, I.162, K.163, E.164, F.165, T.166 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.80, A:R.80, A:N.83, A:I.106, A:S.107, A:E.164, A:T.166, A:T.166 Water bridges: A:S.34, A:S.34 Salt bridges: A:R.66, A:R.66, A:R.80 pi-Stacking: A:F.75, A:F.165 ADX.8: 17 residues within 4Å: Chain B: S.34, R.66, F.75, R.80, N.83, I.84, F.105, I.106, S.107, P.108, K.151, L.153, I.162, K.163, E.164, F.165, T.166 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:R.80, B:R.80, B:N.83, B:I.106, B:S.107, B:K.151, B:K.151, B:E.164, B:T.166 Salt bridges: B:R.66, B:R.66, B:R.80 pi-Stacking: B:F.75, B:F.75 ADX.13: 16 residues within 4Å: Chain C: S.34, R.66, F.75, R.80, N.83, I.84, F.105, I.106, S.107, P.108, L.153, I.162, K.163, E.164, F.165, T.166 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:R.80, C:R.80, C:N.83, C:I.106, C:S.107, C:E.164, C:T.166 Water bridges: C:S.34, C:S.34 Salt bridges: C:R.66, C:R.66, C:R.80 pi-Stacking: C:F.75, C:F.165 ADX.16: 17 residues within 4Å: Chain D: S.34, R.66, F.75, R.80, N.83, I.84, F.105, I.106, S.107, P.108, L.153, I.162, K.163, E.164, F.165, T.166 Ligands: ADP.15 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:R.80, D:R.80, D:N.83, D:I.106, D:S.107, D:E.164, D:T.166, D:T.166 Water bridges: D:K.151 Salt bridges: D:R.66, D:R.66, D:R.80 pi-Stacking: D:F.75, D:F.75

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

ADP.7: 13 residues within 4Å: Chain B: L.33, S.34, A.35, S.36, G.37, K.38, S.39, T.40, R.148, P.150, N.184, L.187, V.189 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:A.35, B:S.36, B:G.37, B:K.38, B:S.39, B:T.40, B:T.40, B:L.187 Water bridges: B:K.38, B:K.38, B:K.151, B:K.151, B:N.184, B:N.184, B:N.184, B:L.187 Salt bridges: B:K.38 pi-Cation interactions: B:R.148 ADP.15: 13 residues within 4Å: Chain D: L.33, S.34, A.35, S.36, G.37, K.38, S.39, T.40, R.148, P.150, N.184, L.187 Ligands: ADX.16 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:A.35, D:S.36, D:G.37, D:K.38, D:S.39, D:T.40, D:T.40, D:L.187 Water bridges: D:K.38, D:K.38, D:K.38, D:N.184, D:N.184, D:N.184, D:L.187 Salt bridges: D:K.38 pi-Cation interactions: D:R.148, D:R.148

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 3 residues within 4Å: Chain B: P.188, V.189, Q.190 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.189, B:Q.190 GOL.14: 5 residues within 4Å: Chain C: F.7, R.21, P.132, K.203, Y.205 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.21, C:R.21, C:Y.205 Water bridges: C:F.7, C:E.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lansdon, E.B. et al., Ligand-Induced Structural Changes in Adenosine 5'-Phosphosulfate Kinase from Penicillium chrysogenum. Biochemistry (2002)

Release Date

2002-11-27

Peptides

Adenylylsulfate kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Adenylylsulfate kinase

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