SMTL ID : 9l14.1

Crystal structure of the monobody CL-1 in complex with the Escherichia coli adenylate kinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

hetero-1-1-mer

Ligands

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

AP5.1: 34 residues within 4Å: Chain A: P.9, G.10, A.11, G.12, K.13, G.14, T.15, T.31, G.32, L.35, R.36, M.53, K.57, L.58, V.59, V.64, G.85, F.86, R.88, Q.92, R.119, I.120, R.123, V.132, Y.133, H.134, F.137, R.167, G.198, K.200, P.201, V.202, V.205 Ligands: MG.2 38 PLIP interactions: 38 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:K.57, A:V.59, A:R.88, A:Q.92, A:Q.92, A:R.119, A:Y.133, A:R.156, A:K.200, A:V.202 Water bridges: A:K.13, A:K.13, A:S.30, A:G.32, A:G.32, A:R.36, A:R.119, A:R.119, A:R.123, A:R.167 Salt bridges: A:K.13, A:K.13, A:R.36, A:R.88, A:R.88, A:R.123, A:R.123, A:R.167 pi-Cation interactions: A:R.88, A:R.119

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

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakamura, I. et al., Binding mechanism of adenylate kinase-specific monobodies. Febs Lett. (2025)

Release Date

2025-06-04

Peptides

Adenylate kinase: A
Monobody CL-1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Adenylate kinase

Monobody CL-1

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