SMTL ID : 3dkv.1

Crystal structure of adenylate kinase variant AKlse1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 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-covalent)

MG.2: 3 residues within 4Å: Chain A: G.14 Ligands: AP5.3, EDO.6 No protein-ligand interaction detected (PLIP)

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

AP5.3: 37 residues within 4Å: Chain A: L.8, 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, R.160, R.171, G.197, Q.199, I.201, V.204 Ligands: MG.2, EDO.4, EDO.6 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: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:A.11, A:T.31, A:G.32, A:G.32, A:G.32, A:R.88, A:R.88, A:R.123, A:R.123, A:R.127, A:R.127, A:R.160, 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

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 4 residues within 4Å: Chain A: F.141, D.200, I.201 Ligands: AP5.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.201 Water bridges: A:Q.202 EDO.5: 5 residues within 4Å: Chain A: H.28, I.29, S.30, M.34, R.71 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.30, A:S.30, A:R.71, A:R.71 EDO.6: 8 residues within 4Å: Chain A: G.14, S.30, D.33, R.36, D.84, R.160 Ligands: MG.2, AP5.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.30, A:R.36, A:R.160 Water bridges: A:D.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bannen, R.M. et al., Crystal structure of adenylate kinase variant AKlse1. To be Published

Release Date

2009-06-09

Peptides

Adenylate kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Adenylate kinase

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