SMTL ID : 4mkh.1

Crystal structure of a stable adenylate kinase variant AKv18

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.132, C.135, C.152, D.155 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.132, A:C.135, A:C.152, A:D.155, A:D.155

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

AP5.2: 34 residues within 4Å: Chain A: L.10, P.11, G.12, A.13, G.14, K.15, G.16, T.17, T.33, G.34, F.37, R.38, Y.54, I.55, E.59, L.60, V.61, T.66, G.87, F.88, R.90, Q.94, R.125, L.126, R.129, T.138, Y.139, H.140, F.143, R.162, R.173, G.199, R.201, I.203 40 PLIP interactions: 40 interactions with chain A Hydrogen bonds: A:G.12, A:A.13, A:G.14, A:K.15, A:G.16, A:T.17, A:T.17, A:T.33, A:Y.54, A:V.61, A:T.66, A:Q.94, A:Q.94, A:R.125, A:R.201 Water bridges: A:T.33, A:G.34, A:D.86, A:R.125, A:R.125, A:R.125, A:R.129, A:R.129, A:R.173, A:N.177 Salt bridges: A:K.15, A:K.15, A:K.15, A:R.38, A:R.90, A:R.90, A:R.129, A:R.129, A:R.162, A:R.173, A:R.173 pi-Stacking: A:F.37 pi-Cation interactions: A:R.90, A:R.125, A:R.125

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: M.8, G.9, L.10, R.90, N.177, M.181 Ligands: EDO.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.9, A:G.9 Water bridges: A:L.10, A:R.90, A:N.177 EDO.4: 9 residues within 4Å: Chain A: L.7, M.8, G.9, K.15, G.87, F.88, P.89, R.90 Ligands: EDO.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.7, A:G.9, A:G.9, A:G.87, A:F.88 EDO.5: 4 residues within 4Å: Chain A: N.4, G.106, R.107, P.108 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.4, A:G.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moon, S. et al., An integrated approach for thermal stabilization of a mesophilic adenylate kinase. Proteins (2014)

Release Date

2014-03-26

Peptides

Adenylate kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Adenylate kinase