SMTL ID : 4c5b.1

The X-ray crystal structure of D-alanyl-D-alanine ligase in complex with ATP and D-ala-D-ala

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 23 residues within 4Å: Chain A: K.121, I.166, K.168, E.172, G.173, S.174, S.175, M.178, E.204, K.205, W.206, L.207, E.211, F.233, Y.234, K.239, D.281, M.283, L.293, E.294 Ligands: CO3.4, MG.5, MG.6 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:K.168, A:G.173, A:S.174, A:S.175, A:E.204, A:L.207, A:E.211, A:Y.234, A:E.294 Water bridges: A:E.211, A:E.211, A:K.239, A:K.239, A:D.281 Salt bridges: A:K.121, A:K.121, A:K.168, A:K.239, A:K.239 ADP.10: 23 residues within 4Å: Chain B: K.121, I.166, K.168, E.172, G.173, S.174, S.175, M.178, E.204, K.205, W.206, L.207, E.211, F.233, Y.234, K.239, D.281, M.283, L.293, E.294 Ligands: CO3.13, MG.14, MG.15 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:K.168, B:G.173, B:S.174, B:S.175, B:E.204, B:L.207, B:E.211, B:Y.234 Water bridges: B:E.211, B:K.239, B:K.239 Salt bridges: B:K.121, B:K.121, B:K.168, B:K.239, B:K.239

4 x DAL: D-ALANINE(Non-covalent)

DAL.2: 10 residues within 4Å: Chain A: E.39, V.42, H.87, S.174, Y.240, R.279, P.299, G.300 Ligands: DAL.3, CO3.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.42, A:H.87 Hydrogen bonds: A:E.39, A:S.174, A:R.279, A:R.279, A:G.300 DAL.3: 9 residues within 4Å: Chain A: Y.234, K.239, Y.240, R.279, G.300, S.305, L.306 Ligands: DAL.2, CO3.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:K.239, A:L.306 Hydrogen bonds: A:Y.240, A:Y.240, A:Y.240, A:L.306 Water bridges: A:V.307 Salt bridges: A:R.279 DAL.11: 10 residues within 4Å: Chain B: E.39, V.42, H.87, S.174, Y.240, R.279, P.299, G.300 Ligands: DAL.12, CO3.13 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.42, B:H.87 Hydrogen bonds: B:E.39, B:R.279, B:R.279, B:G.300 DAL.12: 9 residues within 4Å: Chain B: Y.234, K.239, Y.240, R.279, G.300, S.305, L.306 Ligands: DAL.11, CO3.13 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:K.239 Hydrogen bonds: B:Y.240, B:Y.240, B:Y.240, B:G.300, B:L.306 Water bridges: B:R.279, B:V.307 Salt bridges: B:R.279

2 x CO3: CARBONATE ION(Non-functional Binders)

CO3.4: 12 residues within 4Å: Chain A: G.173, S.174, K.239, R.279, D.281, E.294, N.296 Ligands: ADP.1, DAL.2, DAL.3, MG.5, MG.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.174, A:K.239, A:E.294 CO3.13: 13 residues within 4Å: Chain B: G.173, S.174, K.239, Y.240, R.279, D.281, E.294, N.296 Ligands: ADP.10, DAL.11, DAL.12, MG.14, MG.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.174, B:K.239, B:N.296

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.5: 6 residues within 4Å: Chain A: G.173, E.294, N.296 Ligands: ADP.1, CO3.4, MG.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.294, A:E.294, H2O.10 MG.6: 6 residues within 4Å: Chain A: K.239, D.281, E.294 Ligands: ADP.1, CO3.4, MG.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.281, A:E.294, H2O.13 MG.14: 7 residues within 4Å: Chain B: K.121, G.173, E.294, N.296 Ligands: ADP.10, CO3.13, MG.15 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.294, B:E.294, H2O.24 MG.15: 7 residues within 4Å: Chain B: K.239, D.281, E.294, N.296 Ligands: ADP.10, CO3.13, MG.14 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.281, B:E.294, H2O.27 MG.16: 1 residues within 4Å: Chain B: H.304 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:H.304, H2O.27, H2O.27, H2O.29, H2O.29, H2O.30 MG.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: E.41, V.42, N.45, Y.236, Y.240, L.241 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.41, A:N.45, A:Y.236 GOL.8: 4 residues within 4Å: Chain A: N.185, Q.188, D.189, R.192 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.189, A:R.192

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.9: 4 residues within 4Å: Chain A: K.239, Y.240, S.242, H.304 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.242 Water bridges: A:S.242

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Batson, S. et al., Inhibition of D-Ala:D-Ala ligase through a phosphorylated form of the antibiotic D-cycloserine. Nat Commun (2017)

Release Date

2015-01-21

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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