SMTL ID : 7owk.2 (1 other biounit)

Odinarchaeota Adenylate kinase (OdinAK) in complex with dTTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-trimer

Ligands

3 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.1: 15 residues within 4Å: Chain A: V.8, P.9, G.10, A.11, G.12, K.13, T.14, T.15, R.124, D.128, R.134, Q.176, E.179, F.180, T.183 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.180, A:T.183 Hydrogen bonds: A:G.10, A:A.11, A:G.12, A:K.13, A:T.14, A:T.14, A:T.14, A:T.15, A:T.15, A:R.124, A:D.128, A:Q.176, A:E.179, A:F.180 Water bridges: A:K.133 Salt bridges: A:R.134 pi-Cation interactions: A:R.124 TTP.2: 14 residues within 4Å: Chain B: P.9, G.10, A.11, G.12, K.13, T.14, T.15, R.124, K.127, D.128, Q.176, E.179, F.180, T.183 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:T.183 Hydrogen bonds: B:G.10, B:A.11, B:G.12, B:K.13, B:T.14, B:T.14, B:T.14, B:T.15, B:T.15, B:D.128, B:Q.176, B:E.179, B:F.180 Salt bridges: B:K.13 pi-Stacking: B:F.180 pi-Cation interactions: B:R.124 TTP.3: 17 residues within 4Å: Chain C: P.9, G.10, A.11, G.12, K.13, T.14, T.15, H.85, R.124, K.127, D.128, R.134, Q.176, E.179, F.180, H.182, T.183 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:T.15, C:F.180 Hydrogen bonds: C:G.10, C:A.11, C:T.14, C:T.14, C:T.15, C:T.15, C:H.85, C:R.124, C:K.127, C:D.128, C:Q.176, C:E.179, C:F.180, C:H.182 Water bridges: C:R.134, C:R.134 Salt bridges: C:K.13, C:K.13, C:R.134 pi-Stacking: C:F.180 pi-Cation interactions: C:R.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Verma, A. et al., Insights into the evolution of enzymatic specificity and catalysis: From Asgard archaea to human adenylate kinases. Sci Adv (2022)

Release Date

2022-09-28

Peptides

Adenylate kinase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Adenylate kinase

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