SMTL ID : 2wkx.1

Crystal structure of the native E. coli zinc amidase AmiD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.35, H.151, D.161 Ligands: CL.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.35, A:H.151, A:D.161, A:D.161 ZN.8: 4 residues within 4Å: Chain B: H.35, H.151, D.161 Ligands: CL.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.35, B:H.151, B:D.161, B:D.161

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

CL.2: 5 residues within 4Å: Chain A: A.85, G.86, H.151, R.158, K.159 Ligand excluded by PLIP CL.3: 5 residues within 4Å: Chain A: H.35, H.151, K.159, D.161 Ligands: ZN.1 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain B: A.85, G.86, H.151, R.158, K.159 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain B: H.35, H.151, K.159, D.161 Ligands: ZN.8 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: A.201, L.204, V.214, K.215, P.216, D.217, M.218 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.218 GOL.5: 8 residues within 4Å: Chain A: P.145, A.172, G.175, I.176, G.177, K.257, Y.258 Ligands: GOL.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.172, A:G.175, A:K.257, A:Y.258 GOL.6: 7 residues within 4Å: Chain A: A.172, Q.173, W.179, P.180, D.181, K.257 Ligands: GOL.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:P.180, A:D.181, A:K.257, A:Y.258, A:Y.258 Water bridges: A:Q.173, A:A.182 GOL.7: 8 residues within 4Å: Chain A: V.31, W.90, R.91, A.93, L.96, N.147, D.261 Chain B: R.95 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:W.90, A:N.147, A:D.261, B:R.95, B:R.95 GOL.11: 7 residues within 4Å: Chain B: A.201, L.204, V.214, K.215, P.216, D.217, M.218 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.218 Water bridges: B:Q.223 GOL.12: 8 residues within 4Å: Chain B: P.145, A.172, G.175, I.176, G.177, K.257, Y.258 Ligands: GOL.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.172, B:G.175, B:K.257 GOL.13: 7 residues within 4Å: Chain B: A.172, Q.173, W.179, P.180, D.181, K.257 Ligands: GOL.12 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:P.180, B:K.257, B:Y.258, B:Y.258 Water bridges: B:Q.173, B:A.182 GOL.14: 8 residues within 4Å: Chain A: R.95 Chain B: V.31, W.90, R.91, A.93, L.96, N.147, D.261 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:W.90, B:N.147, B:D.261, A:R.95, A:R.95 Water bridges: B:D.261

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kerff, F. et al., Specific Structural Features of the N-Acetylmuramoyl-L-Alanine Amidase Amid from Escherichia Coli and Mechanistic Implications for Enzymes of This Family. J.Mol.Biol. (2010)

Release Date

2010-01-12

Peptides

N-ACETYLMURAMOYL-L-ALANINE AMIDASE AMID: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

N-ACETYLMURAMOYL-L-ALANINE AMIDASE AMID

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