SMTL ID : 3dl0.1 (1 other biounit)

Crystal structure of adenylate kinase variant AKlse3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.58 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, D.153 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.130, A:C.133, A:C.150, A:D.153

1 x MG: MAGNESIUM ION(Non-covalent)

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

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

AP5.3: 33 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, I.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, R.160, R.171, G.197, Q.199, I.201 Ligands: MG.2 47 PLIP interactions: 47 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:T.64, A:R.88, A:Q.92, A:Q.92, A:R.123, A:Y.137, A:Q.199 Water bridges: A:A.11, A:K.13, A:G.32, A:R.88, A:R.88, A:R.123, A:R.123, A:R.127, A:R.127, A:T.136, A:N.142, A:R.160, A:R.160, A:N.175 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.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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moon, S. et al., Effectiveness and limitations of local structural entropy optimization in the thermal stabilization of mesophilic and thermophilic adenylate kinases. Proteins (2014)

Release Date

2009-06-09

Peptides

Adenylate kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Adenylate kinase

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