SMTL ID : 5x6i.1

Crystal structure of B. subtilis adenylate kinase variant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 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: 35 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, D.162, R.171, G.197, Q.199, I.201 Ligands: MG.2 49 PLIP interactions: 49 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:T.64, 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:G.56, A:D.84, A:R.88, A:R.88, A:R.123, A:R.123, A:R.127, A:R.127, A:R.160, A:D.162, A:N.175 Salt bridges: A:K.13, A:K.13, A:K.13, A:R.36, 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

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 1 residues within 4Å: Chain A: E.41 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.41, H2O.3 CA.5: 2 residues within 4Å: Chain A: D.116, D.118 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.116, A:D.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moon, S. et al., Structural and mutational analyses of psychrophilic and mesophilic adenylate kinases highlight the role of hydrophobic interactions in protein thermal stability. Struct Dyn. (2019)

Release Date

2018-02-28

Peptides

Adenylate kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Adenylate kinase