SMTL ID : 3x2s.1 (1 other biounit)

Crystal structure of pyrene-conjugated adenylate kinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

2 x JPY: N-(pyren-1-ylmethyl)acetamide(Covalent)

JPY.1: 6 residues within 4Å: Chain A: C.55, K.57, K.166, C.169, E.170 Ligands: JPY.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.57, A:K.166, A:K.166, A:K.166 Hydrogen bonds: A:K.166 pi-Cation interactions: A:K.166 JPY.2: 4 residues within 4Å: Chain A: C.169, E.170, Q.173 Ligands: JPY.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.173

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

AP5.3: 36 residues within 4Å: Chain A: P.9, G.10, A.11, G.12, K.13, G.14, T.15, T.31, G.32, L.35, R.36, M.53, K.57, L.58, V.59, V.64, D.84, G.85, F.86, R.88, Q.92, R.119, I.120, R.123, V.132, Y.133, H.134, F.137, R.156, R.167, G.198, K.200, P.201, V.202, V.205 Ligands: MG.4 45 PLIP interactions: 45 interactions with chain A Hydrogen bonds: A:G.10, A:A.11, A:G.12, A:G.12, A:K.13, A:G.14, A:T.15, A:T.15, A:T.31, A:M.53, A:K.57, A:V.59, A:R.88, A:R.88, A:Q.92, A:Q.92, A:R.119, A:Y.133, A:K.200, A:V.202 Water bridges: A:K.13, A:K.13, A:R.36, A:R.36, A:R.88, A:R.88, A:R.156, A:R.156, A:R.156 Salt bridges: A:K.13, A:K.13, A:K.13, A:R.36, A:R.88, A:R.88, A:R.123, A:R.123, A:R.123, A:R.156, A:R.156, A:R.156, A:R.167, A:R.167 pi-Cation interactions: A:R.88, A:R.119

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: G.14, D.84 Ligands: AP5.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fujii, A. et al., Excimer Emission Properties on Pyrene-Labeled Protein Surface: Correlation between Emission Spectra, Ring Stacking Modes, and Flexibilities of Pyrene Probes. Bioconjug.Chem. (2015)

Release Date

2015-04-01

Peptides

Adenylate kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Adenylate kinase

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