SMTL ID : 2rgx.1

Crystal Structure of Adenylate Kinase from Aquifex Aeolicus in complex with Ap5A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

4 x ZN: ZINC ION(Non-functional Binders)(Non-covalent)

ZN.1: 1 residues within 4Å: Ligands: AP5.5 No protein-ligand interaction detected (PLIP) ZN.2: 2 residues within 4Å: Chain A: E.163, E.167 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.163, A:E.167, A:E.167 ZN.3: 2 residues within 4Å: Chain A: E.95, E.98 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.95, A:E.95, A:E.98, H2O.4 ZN.4: 2 residues within 4Å: Chain A: H.106, I.202 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.106, H2O.4

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

AP5.5: 35 residues within 4Å: Chain A: P.8, P.9, G.10, A.11, G.12, K.13, G.14, T.15, T.31, G.32, L.35, R.36, M.53, E.57, L.58, V.59, I.64, G.82, F.83, R.85, Q.89, R.120, L.121, R.124, V.133, Y.134, H.135, Y.138, R.150, R.161, K.189, P.190, V.191, V.194 Ligands: ZN.1 44 PLIP interactions: 44 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:T.31, A:G.32, A:R.36, A:E.57, A:V.59, A:R.85, A:Q.89, A:Q.89, A:R.120, A:R.150, A:K.189 Water bridges: A:G.7, A:K.13, A:K.13, A:K.13, A:T.15, A:R.120, A:R.120, A:R.120, A:R.120, A:R.124, A:R.124, A:N.139, A:R.150, A:R.150, A:V.191 Salt bridges: A:K.13, A:K.13, A:K.13, A:R.124, A:R.124, A:R.150, A:R.161, A:R.161 pi-Cation interactions: A:R.85, A:R.85, A:R.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Henzler-Wildman, K.A. et al., Intrinsic motions along an enzymatic reaction trajectory. Nature (2007)

Release Date

2007-12-18

Peptides

Adenylate kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Adenylate kinase

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