SMTL ID : 3sr0.1 (1 other biounit)

Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: ADP/AlF4/AMP in the active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

monomer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 23 residues within 4Å: Chain A: P.9, G.10, A.11, G.12, K.13, G.14, T.15, Q.16, R.120, L.121, R.124, R.125, V.133, Y.134, H.135, Y.138, N.139, K.189, P.190, V.191, V.194 Ligands: MG.3, ALF.4 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:G.10, A:A.11, A:G.12, A:K.13, A:G.14, A:T.15, A:T.15, A:Y.134, A:Y.134, A:K.189 Water bridges: A:G.14, A:T.15, A:R.120, A:R.124, A:R.124, A:N.139 Salt bridges: A:K.13, A:R.124, A:R.124

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 21 residues within 4Å: Chain A: T.31, G.32, L.35, R.36, Y.52, M.53, G.56, E.57, L.58, V.59, I.64, G.82, F.83, P.84, R.85, Q.89, R.150, D.152, R.161 Ligands: MG.3, ALF.4 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:T.31, A:G.32, A:E.57, A:E.57, A:V.59, A:R.85, A:R.85, A:Q.89, A:Q.89, A:R.161, A:R.161 Water bridges: A:K.13, A:D.33, A:R.36, A:G.56, A:R.85, A:D.152 Salt bridges: A:R.36, A:R.85, A:R.150, A:R.161 pi-Cation interactions: A:R.85

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 6 residues within 4Å: Chain A: G.14, R.124, R.150 Ligands: ADP.1, AMP.2, ALF.4 No protein-ligand interaction detected (PLIP)

1 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.4: 10 residues within 4Å: Chain A: P.9, G.10, K.13, L.121, R.124, R.150, R.161 Ligands: ADP.1, AMP.2, MG.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kerns, S.J. et al., The energy landscape of adenylate kinase during catalysis. Nat.Struct.Mol.Biol. (2015)

Release Date

2012-10-10

Peptides

Adenylate kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Adenylate kinase

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