SMTL ID : 6ln3.1

Crystal structure of adenylate kinase from an extremophilic archaeon Aeropyrum pernix with ATP and AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

3 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 15 residues within 4Å: Chain A: N.40, F.41, G.42, M.45, R.58, I.61, R.62, Q.73, T.98, H.99, V.102, W.109, G.111, R.145 Ligands: ATP.2 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:N.40, A:R.62, A:Q.73, A:T.98, A:T.98 Water bridges: A:K.18, A:K.18, A:T.19, A:F.41, A:G.42, A:R.62, A:H.99, A:R.145, A:R.145, A:R.145, A:R.147 Salt bridges: A:R.58, A:H.99, A:R.145 AMP.6: 15 residues within 4Å: Chain B: N.40, F.41, G.42, M.45, R.58, I.61, R.62, Q.73, T.98, H.99, V.102, W.109, G.111, R.145 Ligands: ATP.7 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:N.40, B:R.62, B:Q.73, B:T.98, B:T.98 Water bridges: B:K.18, B:K.18, B:T.19, B:F.41, B:G.42, B:D.59, B:R.62, B:H.99, B:R.145, B:R.145, B:R.147 Salt bridges: B:R.58, B:H.99, B:R.145 AMP.11: 15 residues within 4Å: Chain C: N.40, F.41, G.42, M.45, R.58, I.61, R.62, Q.73, T.98, H.99, V.102, W.109, G.111, R.145 Ligands: ATP.12 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:N.40, C:R.62, C:Q.73, C:T.98, C:T.98 Water bridges: C:K.18, C:K.18, C:T.19, C:F.41, C:G.42, C:D.59, C:R.62, C:H.99, C:R.145, C:R.145, C:R.147 Salt bridges: C:R.58, C:H.99, C:R.145

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 21 residues within 4Å: Chain A: V.13, P.14, G.15, V.16, G.17, K.18, T.19, T.20, H.99, R.138, D.142, R.145, R.147, N.183, R.184, E.185, G.186, E.187, A.188 Ligands: AMP.1, MG.3 34 PLIP interactions: 34 interactions with chain A Hydrogen bonds: A:G.15, A:V.16, A:G.17, A:K.18, A:T.19, A:T.20, A:T.20, A:D.142, A:D.142, A:N.183, A:R.184, A:G.186, A:E.187 Water bridges: A:K.18, A:T.19, A:T.19, A:T.20, A:N.40, A:N.40, A:H.99, A:R.145, A:R.145, A:R.145, A:R.147, A:R.147, A:A.188 Salt bridges: A:K.18, A:K.18, A:H.99, A:R.145, A:R.147, A:R.147, A:R.147 pi-Cation interactions: A:R.138 ATP.7: 21 residues within 4Å: Chain B: V.13, P.14, G.15, V.16, G.17, K.18, T.19, T.20, H.99, R.138, D.142, R.145, R.147, N.183, R.184, E.185, G.186, E.187, A.188 Ligands: AMP.6, MG.8 33 PLIP interactions: 33 interactions with chain B Hydrogen bonds: B:G.15, B:V.16, B:G.17, B:K.18, B:T.19, B:T.20, B:T.20, B:D.142, B:D.142, B:N.183, B:R.184, B:G.186, B:E.187 Water bridges: B:K.18, B:T.19, B:T.20, B:N.40, B:N.40, B:N.40, B:H.99, B:R.145, B:R.145, B:R.147, B:R.147, B:A.188 Salt bridges: B:K.18, B:K.18, B:H.99, B:R.145, B:R.147, B:R.147, B:R.147 pi-Cation interactions: B:R.138 ATP.12: 21 residues within 4Å: Chain C: V.13, P.14, G.15, V.16, G.17, K.18, T.19, T.20, H.99, R.138, D.142, R.145, R.147, N.183, R.184, E.185, G.186, E.187, A.188 Ligands: AMP.11, MG.13 33 PLIP interactions: 33 interactions with chain C Hydrogen bonds: C:G.15, C:V.16, C:G.17, C:K.18, C:T.19, C:T.19, C:T.20, C:T.20, C:D.142, C:N.183, C:R.184, C:G.186, C:E.187 Water bridges: C:K.18, C:T.20, C:N.40, C:N.40, C:H.99, C:R.145, C:R.145, C:R.145, C:R.145, C:R.147, C:R.147, C:A.188 Salt bridges: C:K.18, C:K.18, C:H.99, C:R.145, C:R.147, C:R.147, C:R.147 pi-Cation interactions: C:R.138

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: T.19 Ligands: ATP.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.19, H2O.2, H2O.2, H2O.3 MG.8: 2 residues within 4Å: Chain B: T.19 Ligands: ATP.7 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.19, H2O.7, H2O.8, H2O.9 MG.13: 2 residues within 4Å: Chain C: T.19 Ligands: ATP.12 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.19, H2O.13, H2O.14, H2O.15

3 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 6 residues within 4Å: Chain A: K.35, S.85, K.86, A.87, L.88, G.89 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.87, A:G.89 Salt bridges: A:K.35 EPE.9: 6 residues within 4Å: Chain B: K.35, S.85, K.86, A.87, L.88, G.89 3 PLIP interactions: 3 interactions with chain B Water bridges: B:A.87, B:G.89 Salt bridges: B:K.35 EPE.14: 6 residues within 4Å: Chain C: K.35, S.85, K.86, A.87, L.88, G.89 3 PLIP interactions: 3 interactions with chain C Water bridges: C:A.87, C:G.89 Salt bridges: C:K.35

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 5 residues within 4Å: Chain A: G.12, H.99, A.100, L.101, A.163 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain B: G.12, H.99, A.100, L.101, A.163 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain C: G.12, H.99, A.100, L.101, A.163 Ligand excluded by PLIP

Links

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Citation

Shibanuma, Y. et al., Crystal structure of adenylate kinase from an extremophilic archaeon Aeropyrum pernix with ATP and AMP. J.Biochem. (2020)

Release Date

2020-04-22

Peptides

Adenylate kinase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Adenylate kinase