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

Odinarchaeota Adenylate kinase (OdinAK) in complex with GTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

3 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 15 residues within 4Å: Chain A: V.8, P.9, G.10, A.11, G.12, K.13, T.14, T.15, H.85, R.124, K.127, D.128, Q.176, E.179, F.180 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:V.8, A:G.10, A:A.11, A:G.12, A:K.13, A:T.14, A:T.14, A:T.15, A:R.124, A:K.127, A:K.127, A:D.128, A:Q.176, A:F.180 Water bridges: A:H.182, A:T.183 Salt bridges: A:K.13, A:K.13, A:H.85, A:E.179 pi-Stacking: A:F.180 pi-Cation interactions: A:F.180 GTP.2: 11 residues within 4Å: Chain B: P.9, G.10, G.12, K.13, T.14, C.17, V.29, N.31, D.34, D.83, H.85 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.10, B:A.11, B:G.12, B:K.13, B:T.14, B:T.14, B:V.29, B:N.31 Salt bridges: B:K.13, B:D.83, B:H.85, B:H.85 GTP.3: 15 residues within 4Å: Chain C: V.8, P.9, G.10, A.11, G.12, K.13, T.14, T.15, H.85, R.124, K.127, D.128, Q.176, E.179, F.180 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:G.10, C:A.11, C:G.12, C:K.13, C:T.14, C:T.15, C:K.127, C:D.128, C:Q.176, C:F.180 Water bridges: C:R.51, C:R.124, C:H.182 Salt bridges: C:K.13, C:K.13, C:H.85, C:E.179 pi-Stacking: C:F.180

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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