SMTL ID : 1m7h.4 (3 other biounits)

Crystal Structure of APS kinase from Penicillium Chrysogenum: Structure with APS soaked out of one dimer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: R.66, R.80, F.105, I.106 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.80, A:I.106 Water bridges: A:R.66, A:N.83, A:S.107 Salt bridges: A:R.66 SO4.2: 5 residues within 4Å: Chain A: R.110, A.174, P.175, A.176, N.177 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:A.176, A:N.177, A:N.177 Water bridges: A:R.113, A:R.117, A:E.135, A:E.135, A:E.135, A:E.135 Salt bridges: A:R.110 SO4.3: 4 residues within 4Å: Chain A: F.7, H.8, A.9, S.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.8, A:A.9, A:S.10, A:S.10 SO4.4: 4 residues within 4Å: Chain A: Y.172, E.173, A.174 Chain D: K.156 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:K.151, A:A.174 Water bridges: D:K.156 Salt bridges: D:K.156 SO4.5: 2 residues within 4Å: Chain A: S.76, E.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.77 SO4.7: 3 residues within 4Å: Chain B: T.13, R.14, S.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.13, B:R.14, B:S.15, B:S.15 SO4.8: 4 residues within 4Å: Chain B: F.7, H.8, A.9, S.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.9, B:S.10, B:S.10 SO4.11: 3 residues within 4Å: Chain C: R.80, F.105, I.106 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.80, C:I.106 Water bridges: C:N.83, C:S.104, C:S.107 SO4.12: 4 residues within 4Å: Chain C: F.7, H.8, A.9, S.10 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:F.7, C:A.9, C:S.10 SO4.13: 5 residues within 4Å: Chain C: R.110, A.174, P.175, A.176, N.177 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:A.176, C:N.177, C:N.177 Water bridges: C:R.113, C:E.135, C:E.135 Salt bridges: C:R.110 SO4.14: 3 residues within 4Å: Chain B: S.76 Chain C: S.76, E.77 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.77 Water bridges: C:A.78 SO4.16: 4 residues within 4Å: Chain D: F.7, H.8, A.9, S.10 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:F.7, D:H.8, D:A.9, D:S.10, D:S.10 Water bridges: D:T.6

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

ADP.6: 13 residues within 4Å: Chain A: 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 19 PLIP interactions: 19 interactions with chain A 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:R.148, A:K.151, A:K.151, A:L.187 Salt bridges: A:K.38 pi-Cation interactions: A:R.148, A:R.148 ADP.9: 12 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 19 PLIP interactions: 19 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:R.148, B:N.184, B:L.187 Water bridges: B:K.38, B:K.38, B:S.39, B:S.39, B:S.39, B:L.187, B:L.187 Salt bridges: B:K.38 pi-Cation interactions: B:R.148 ADP.15: 12 residues within 4Å: 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 18 PLIP interactions: 18 interactions with chain C 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:K.151, C:K.151, C:L.187 Salt bridges: C:K.38 pi-Cation interactions: C:R.148, C:R.148 ADP.17: 12 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 17 PLIP interactions: 17 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:R.148, D:N.184, D:L.187 Water bridges: D:K.38, D:K.38, D:S.104, D:L.187, D:L.187 Salt bridges: D:K.38 pi-Cation interactions: D:R.148

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

ADX.10: 16 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, L.153, I.162, K.163, E.164, F.165, T.166 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.80, B:N.83, B:I.106, B:S.107, B:E.164, B:T.166 Water bridges: B:S.34, B:A.35 Salt bridges: B:R.66, B:R.66, B:R.80 ADX.18: 16 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 13 PLIP interactions: 13 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:S.34 Salt bridges: D:R.66, D:R.66, D:R.80 pi-Stacking: D:F.75

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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