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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 15 residues within 4Å: Chain A: K.97, I.142, K.144, E.148, M.154, E.180, K.181, W.182, L.183, E.187, F.209, Y.210, M.259, L.269, E.270 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.144, A:E.148, A:E.180, A:E.180, A:L.183, A:E.187, A:Y.210, A:E.270 Water bridges: A:E.187 Salt bridges: A:K.97, A:K.144 AMP.7: 13 residues within 4Å: Chain B: K.97, I.142, K.144, E.180, K.181, W.182, L.183, E.187, F.209, Y.210, M.259, L.269, E.270 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:K.144, B:E.180, B:L.183, B:E.187, B:Y.210, B:E.270, B:E.270 Water bridges: B:K.144, B:E.187, B:K.215, B:D.257, B:L.269 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.68, A:T.94 NA.6: 1 residues within 4Å: Chain A: H.280 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.280 NA.8: 5 residues within 4Å: Chain B: E.68, S.91, T.94, M.95, T.273 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.68

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 6 residues within 4Å: Chain A: Y.210, K.215, R.255, G.276, S.281, L.282 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:K.215, A:L.282 Hydrogen bonds: A:G.276, A:L.282 Water bridges: A:Y.210, A:Y.210, A:V.283 Salt bridges: A:R.255 ACT.9: 7 residues within 4Å: Chain B: Y.210, K.215, R.255, G.276, S.281, L.282 Ligands: ACT.12 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.215 Hydrogen bonds: B:L.282 Water bridges: B:V.283 Salt bridges: B:R.255 ACT.12: 6 residues within 4Å: Chain B: K.215, R.255, N.272, P.275, G.276 Ligands: ACT.9 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.215 Hydrogen bonds: B:G.276 Water bridges: B:N.272 Salt bridges: B:H.63, B:R.255

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: L.76, E.77, Q.80, L.81, Y.83, D.306 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.77, A:D.306 Water bridges: A:E.77, A:E.77 GOL.5: 6 residues within 4Å: Chain A: L.107, H.246, A.247 Chain B: L.98, A.116, N.118 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.99, B:N.118, A:H.246 Water bridges: B:D.176 GOL.10: 8 residues within 4Å: Chain B: P.82, Y.83, G.85, S.86, G.87, S.251, D.306 Ligands: GOL.11 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.83, B:S.251, B:D.306 Water bridges: B:G.85, B:G.87, B:S.251, B:S.251, B:D.306 GOL.11: 8 residues within 4Å: Chain B: L.76, E.77, Q.80, L.81, P.82, Y.83, D.306 Ligands: GOL.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.80, B:D.306 Water bridges: B:E.77, B:E.77

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
D

D-alanine--D-alanine ligase

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