SMTL ID : 1xqi.1 (2 other biounits)

Crystal Structure Analysis of an NDP kinase from Pyrobaculum aerophilum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 6 residues within 4Å: Chain A: K.23, Y.63, T.138, N.169, H.172 Ligands: PGE.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.23, A:Y.63, A:Y.63, A:T.138, A:N.169, A:N.169 TRS.3: 7 residues within 4Å: Chain B: K.23, Y.63, T.138, N.169, V.171, H.172 Ligands: PGE.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.23, B:Y.63, B:N.169, B:N.169, B:H.172

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 10 residues within 4Å: Chain A: Y.63, P.64, W.69, H.172, A.173, S.174, D.175, E.179, E.183 Ligands: TRS.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.172, A:D.175, A:E.179 PGE.4: 10 residues within 4Å: Chain B: Y.63, P.64, W.69, H.172, A.173, S.174, D.175, E.179, E.183 Ligands: TRS.3 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.175, B:D.175, B:E.179, B:E.183 Water bridges: B:R.132, B:A.173, B:A.173, B:R.182, B:R.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pedelacq, J.D. et al., Structural and functional features of an NDP kinase from the hyperthermophile crenarchaeon Pyrobaculum aerophilum. Protein Sci. (2005)

Release Date

2005-09-20

Peptides

Nucleoside diphosphate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Nucleoside diphosphate kinase

Related Entries With Identical Sequence