SMTL ID : 5g3z.1

Crystal structure of adenylate kinase ancestor 3 with Zn, Mg and Ap5A bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.130, C.133, C.150, C.153 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.130, A:C.133, A:C.150, A:C.153

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

AP5.2: 36 residues within 4Å: Chain A: P.9, G.10, A.11, G.12, K.13, G.14, T.15, T.31, G.32, F.35, R.36, M.53, E.57, L.58, V.59, T.64, G.85, F.86, R.88, Q.92, R.123, L.124, R.127, T.136, Y.137, H.138, F.141, N.142, R.160, D.162, R.171, G.197, Q.199, D.200, I.201 Ligands: MG.3 48 PLIP interactions: 48 interactions with chain A Hydrogen bonds: A:G.10, A:G.12, A:K.13, A:G.14, A:T.15, A:T.15, A:T.31, A:E.57, A:V.59, A:G.85, A:R.88, A:Q.92, A:R.123, A:R.123, A:T.136, A:T.136, A:N.142, A:Q.199 Water bridges: A:A.11, A:A.11, A:S.30, A:G.32, A:R.36, A:R.88, A:R.88, A:R.123, A:R.123, A:R.127, A:R.127, A:D.162 Salt bridges: A:K.13, A:K.13, A:K.13, A:R.36, A:R.88, A:R.88, A:R.127, A:R.127, A:R.127, A:R.160, A:R.160, A:R.160, A:R.171, A:R.171 pi-Stacking: A:F.35 pi-Cation interactions: A:R.88, A:R.123, A:R.123

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: G.14 Ligands: AP5.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, V. et al., Evolutionary drivers of thermoadaptation in enzyme catalysis. Science (2017)

Release Date

2016-12-28

Peptides

ADENYLATE KINSE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ADENYLATE KINSE