SMTL ID : 4mkf.2 (1 other biounit)

Crystal structure of a stable adenylate kinase variant AKv3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 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 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.130, A:C.133, A:C.150, A:D.153, A:D.153

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

MG.2: 1 residues within 4Å: Ligands: AP5.3 No protein-ligand interaction detected (PLIP)

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

AP5.3: 34 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, N.142, 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:G.32, A:E.57, A:V.59, A:R.88, A:R.88, A:Q.92, A:Q.92, A:R.123, A:R.123, A:T.136, A:T.136, A:N.142, A:Q.199 Water bridges: A:R.36, A:R.88, A:R.88, A:R.123, A:R.123, A:R.127, A:R.127, A:R.160, A:R.160, A:N.175 Salt bridges: A:K.13, A:K.13, A:K.13, A:R.88, A:R.88, A:R.127, 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

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 1 residues within 4Å: Chain A: D.200 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.200, H2O.9, H2O.9, H2O.9, H2O.9 CA.5: 1 residues within 4Å: Chain A: D.200 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.200, A:D.200, H2O.1, H2O.3, H2O.10 CA.6: 1 residues within 4Å: Chain A: Q.199 No protein-ligand interaction detected (PLIP) CA.7: 1 residues within 4Å: Chain A: K.40 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:K.40, H2O.4, H2O.8, H2O.9, H2O.9

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
B

Adenylate kinase

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