SMTL ID : 5c1o.1 (1 other biounit)

Crystal structure of AMP-PNP complexed D-alanine-D-alanine ligase(DDL) from Yersinia pestis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 16 residues within 4Å: Chain A: K.97, I.142, K.144, M.154, E.180, K.181, W.182, L.183, E.187, Y.210, D.211, Y.212, M.259, L.269, E.270 Ligands: MG.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.97, A:S.112, A:K.144, A:K.181, A:L.183, A:E.187, A:Y.210, A:Y.212 Salt bridges: A:K.97, A:K.144 ANP.4: 14 residues within 4Å: Chain B: K.97, I.142, K.144, E.148, S.151, M.154, E.180, K.181, W.182, L.183, E.187, M.259, E.270 Ligands: MG.6 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:K.97, B:K.144, B:E.148, B:E.148, B:S.151, B:S.151, B:E.180, B:K.181, B:L.183, B:E.187 Salt bridges: B:K.97, B:K.144

3 x NA: SODIUM ION(Non-functional Binders)

NA.2: 5 residues within 4Å: Chain A: E.68, S.91, T.94, M.95, T.273 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.94 NA.5: 5 residues within 4Å: Chain B: E.68, S.91, T.94, M.95, T.273 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.94, B:T.273 NA.7: 1 residues within 4Å: Chain B: H.265 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.265

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: K.97, E.270 Ligands: ANP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.270 MG.6: 4 residues within 4Å: Chain B: K.97, E.148, E.270 Ligands: ANP.4 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.148, B:E.148, B:E.270, B:E.270

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tran, H.T. et al., Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop. Acta Crystallogr D Struct Biol (2016)

Release Date

2016-03-02

Peptides

D-alanine--D-alanine ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-alanine--D-alanine ligase

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