SMTL ID : 4buc.1 (1 other biounit)

CRYSTAL STRUCTURE OF MURD LIGASE FROM THERMOTOGA MARITIMA IN APO FORM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

monomer

Ligands

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 8 residues within 4Å: Chain A: G.129, K.133, S.177, S.178, F.179, D.203, Y.211, K.215 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.129, A:G.129, A:S.178, A:S.178, A:Y.211 Water bridges: A:G.129, A:E.175 Salt bridges: A:K.133, A:K.215 PO4.2: 6 residues within 4Å: Chain A: G.132, T.135, Q.278, M.279, N.282 Ligands: GOL.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.135, A:T.135, A:N.282 PO4.3: 5 residues within 4Å: Chain A: N.196, N.231, H.233, Y.277, E.281 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.196, A:N.231, A:N.231 Water bridges: A:E.281, A:E.281 Salt bridges: A:H.233 PO4.4: 3 residues within 4Å: Chain A: D.120, K.123, E.168 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.168, A:E.168 Water bridges: A:D.120, A:D.120, A:K.123, A:K.123, A:K.123 Salt bridges: A:K.123 PO4.5: 6 residues within 4Å: Chain A: G.29, K.30, S.31, S.88, P.89 Ligands: NH4.16 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.30, A:S.31, A:S.88 Water bridges: A:G.29, A:N.32 PO4.6: 4 residues within 4Å: Chain A: F.403, E.404, M.407, H.445 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.404 Salt bridges: A:H.445 PO4.7: 7 residues within 4Å: Chain A: Y.86, K.107, S.109, Q.113, F.114, D.117, E.185 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.86, A:S.109, A:D.117, A:D.117, A:D.117 Salt bridges: A:K.107 PO4.8: 5 residues within 4Å: Chain A: A.52, H.75, I.91 Ligands: PO3.9, CL.15 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.95 Salt bridges: A:H.75

1 x PO3: PHOSPHITE ION(Non-covalent)

PO3.9: 5 residues within 4Å: Chain A: H.75, T.95, S.96, M.97 Ligands: PO4.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.96, A:S.96 Water bridges: A:T.95

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 4 residues within 4Å: Chain A: I.395, V.396, E.397, E.401 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.397, A:E.401 GOL.11: 5 residues within 4Å: Chain A: R.33, K.37, E.58, T.59, F.62 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.33, A:E.58 GOL.12: 6 residues within 4Å: Chain A: D.131, G.132, K.133, S.134, T.135 Ligands: PO4.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.132, A:K.133, A:K.133, A:S.134, A:T.135, A:T.135

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.13: 5 residues within 4Å: Chain A: E.111, G.155, P.160, A.161, Q.180 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain A: F.28, G.29, E.51, K.53 Ligands: CL.15 Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain A: G.27, E.51, A.52, H.75 Ligands: PO4.8, CL.14 Ligand excluded by PLIP

1 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.16: 3 residues within 4Å: Chain A: S.88, G.90 Ligands: PO4.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Favini-Stabile, S. et al., Mreb and Murg as Scaffolds for the Cytoplasmic Steps of Peptidoglycan Biosynthesis. Environ.Microbiol. (2013)

Release Date

2013-07-17

Peptides

UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE

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