PDBsum entry 5ycc

Transferase

PDB id: 5ycc

Contents

Protein chains

186 a.a.

Ligands

AP5 ×2

SO4 ×2

Waters ×28

PDB id:

5ycc

Name:

Transferase

Title:

Crystal structure of notothenia coriiceps adenylate kinase variant

Structure:

Adenylate kinase. Chain: a, b. Engineered: yes

Source:

Notothenia coriiceps. Organism_taxid: 8208. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.70Å R-factor: 0.171 R-free: 0.223

Authors:

E.Bae,J.Kim,S.Moon

Key ref:

E.Bae et al. Crystal structure of notothenia coriiceps adenylate k variant. To be published, .

Date:

07-Sep-17 Release date: 12-Sep-18

Protein chains

A0A2R2JFU5  (A0A2R2JFU5_9TELE) -  Adenylate kinase isoenzyme 1 from Notothenia coriiceps

Seq: 195 a.a.

Struc: 186 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 2: E.C.2.7.4.3 - adenylate kinase.
• Reaction: AMP + ATP = 2 ADP

AMP + ATP (Bound ligand (Het Group name = AP5) matches with 54.39% similarity) = 2 × ADP

• Enzyme class 3: E.C.2.7.4.6 - nucleoside-diphosphate kinase.
• Reaction:
  1. a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-triphosphate + ADP
  2. a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-deoxyribonucleoside 5'-triphosphate + ADP

ribonucleoside 5'-diphosphate + ATP (Bound ligand (Het Group name = AP5) matches with 54.39% similarity) = 2 × ribonucleoside 5'-triphosphate + ADP

2'-deoxyribonucleoside 5'-diphosphate + ATP (Bound ligand (Het Group name = AP5) matches with 54.39% similarity) = 2'-deoxyribonucleoside 5'-triphosphate + ADP

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site