SMTL ID : 4bxd.1

CRYSTAL STRUCTURE OF AMPDH3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH TETRASACCHARIDE PENTAPEPTIDE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-dimer

Ligands

2 x ALA- FGA- 6CL- DAL: PEPTIDE(Non-covalent)

ALA-FGA-6CL-DAL.1: 19 residues within 4Å: Chain A: L.38, A.43, S.44, R.76, W.78, H.79, A.80, G.81, V.82, N.90, N.92, E.99, H.146, R.153, K.154 Chain B: R.20, D.137 Ligands: MAG-NAG-NAG.3, ZN.5 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.78 Hydrogen bonds: A:R.76, A:R.76, A:H.79, A:G.81, A:N.90, A:N.90, A:N.92, A:E.99, A:K.154, B:R.20, B:R.20 Salt bridges: A:R.153, A:K.154, B:R.20 ALA-FGA-6CL-DAL.2: 21 residues within 4Å: Chain A: R.20, R.88 Chain B: H.25, L.38, A.43, S.44, R.76, W.78, H.79, A.80, G.81, V.82, N.90, N.92, E.99, H.146, R.153, K.154 Ligands: MAG-NAG-NAG.4, MAG-NAG-NAG.4, ZN.6 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.78 Hydrogen bonds: B:R.76, B:H.79, B:A.80, B:G.81, B:N.90, B:N.92, B:E.99, B:K.154 Salt bridges: B:H.146, B:R.153, B:K.154, A:R.20

2 x MAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside(Non-covalent)

MAG-NAG-NAG.3: 19 residues within 4Å: Chain A: Y.26, T.27, A.28, L.29, A.37, L.38, A.43, E.99, A.104, R.105, D.106, D.108, G.109, F.111, G.152, R.153, K.154, S.155 Ligands: ALA-FGA-6CL-DAL.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.27, A:K.154, A:D.106 Water bridges: A:Y.26, A:E.99 MAG-NAG-NAG.4: 20 residues within 4Å: Chain B: Y.26, T.27, A.28, L.29, A.37, L.38, E.99, A.104, R.105, D.106, F.111, G.152, R.153, K.154, S.155, D.156, R.223 Ligands: ALA-FGA-6CL-DAL.2, ALA-FGA-6CL-DAL.2, ZN.6 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.29, B:F.111 Hydrogen bonds: B:K.154, B:G.152 Water bridges: B:Y.26, B:E.99

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: H.25, H.146, K.154, D.156 Ligands: ALA-FGA-6CL-DAL.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.25, A:H.146, A:D.156, H2O.1 ZN.6: 6 residues within 4Å: Chain B: H.25, H.146, K.154, D.156 Ligands: ALA-FGA-6CL-DAL.2, MAG-NAG-NAG.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.25, B:H.146, B:D.156, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, M. et al., Cell-Wall Remodeling by the Zinc-Protease Ampdh3 from Pseudomonas Aeruginosa. J.Am.Chem.Soc. (2013)

Release Date

2013-10-09

Peptides

AMPDH3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

AMPDH3

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