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

Odinarchaeota Adenylate kinase (OdinAK) in complex with inhibitor Ap5a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-trimer

Ligands

3 x AP5: BIS(ADENOSINE)-5'-PENTAPHOSPHATE(Non-covalent)

AP5.1: 29 residues within 4Å: Chain A: P.9, G.10, A.11, G.12, K.13, T.14, T.15, N.31, Y.32, G.33, I.36, R.51, E.52, T.54, R.55, Y.62, Q.66, T.84, H.85, L.88, G.97, R.124, K.127, D.128, R.134, R.137, Q.176, F.180, T.183 35 PLIP interactions: 35 interactions with chain A Hydrogen bonds: A:G.10, A:A.11, A:G.12, A:K.13, A:T.14, A:T.14, A:T.15, A:T.15, A:N.31, A:R.51, A:E.52, A:T.54, A:T.54, A:R.55, A:Q.66, A:T.84, A:G.97, A:K.127, A:D.128, A:R.134, A:Q.176, A:Q.176, A:F.180, A:T.183 Salt bridges: A:K.13, A:K.13, A:K.13, A:H.85, A:H.85, A:R.134, A:R.134, A:R.137 pi-Stacking: A:F.180, A:F.180 pi-Cation interactions: A:R.124 AP5.2: 29 residues within 4Å: Chain B: P.9, G.10, A.11, G.12, K.13, T.14, T.15, Y.32, G.33, I.36, R.51, E.52, T.54, R.55, Y.62, Q.66, T.84, H.85, L.88, G.97, R.124, D.128, R.134, R.137, Q.176, E.179, F.180, H.182, T.183 38 PLIP interactions: 38 interactions with chain B Hydrogen bonds: B:G.10, B:G.12, B:K.13, B:T.14, B:T.14, B:T.15, B:N.31, B:E.52, B:T.54, B:R.55, B:R.55, B:R.55, B:Q.66, B:T.84, B:T.84, B:H.85, B:R.124, B:D.128, B:R.137, B:Q.176, B:Q.176, B:E.179, B:F.180, B:T.183, B:T.183 Salt bridges: B:K.13, B:K.13, B:R.51, B:H.85, B:H.85, B:H.85, B:R.134, B:R.137, B:R.137, B:R.137 pi-Stacking: B:F.180, B:F.180 pi-Cation interactions: B:R.124 AP5.3: 23 residues within 4Å: Chain C: P.9, G.10, G.12, K.13, T.14, T.15, N.31, Y.32, G.33, R.51, R.55, D.83, T.84, H.85, L.88, R.124, K.127, D.128, K.133, Q.176, F.180, H.182, T.183 24 PLIP interactions: 24 interactions with chain C Hydrogen bonds: C:G.10, C:G.12, C:K.13, C:T.14, C:T.15, C:G.33, C:R.51, C:R.55, C:D.83, C:D.83, C:T.84, C:K.127, C:D.128, C:Q.176, C:Q.176, C:F.180, C:T.183 Salt bridges: C:K.133, C:K.133, C:K.133 pi-Stacking: C:F.180, C:F.180 pi-Cation interactions: C:H.85, 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
A

B
B

C
C

Adenylate kinase

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