SMTL ID : 4bxe.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

homo-tetramer

Ligands

4 x AH0- ALA- DGL- API- DAL- DAL: ANHYDROMURAMIC PEPTIDE(Non-covalent)

AH0-ALA-DGL-API-DAL-DAL.1: 22 residues within 4Å: Chain A: Y.26, T.27, A.28, L.29, A.37, R.76, W.78, H.79, A.80, G.81, V.82, N.90, N.92, E.99, H.146, R.153, K.154, D.156 Chain B: R.20, R.87, R.88, D.137 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.37, A:W.78 Hydrogen bonds: A:T.27, A:R.76, A:R.76, A:H.79, A:H.79, A:A.80, A:G.81, A:N.90, A:N.92 Salt bridges: A:R.76, A:H.146, A:R.153, A:K.154, A:K.154, B:R.20, B:R.87 AH0-ALA-DGL-API-DAL-DAL.2: 22 residues within 4Å: Chain A: R.20, R.88, D.137 Chain B: H.25, Y.26, T.27, A.28, L.29, A.37, A.43, R.76, W.78, H.79, A.80, G.81, N.90, N.92, E.99, H.146, R.153, K.154, D.156 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.29, B:A.37, B:W.78 Hydrogen bonds: B:H.25, B:T.27, B:R.76, B:W.78, B:G.81, B:N.90, B:N.92, A:R.20 Salt bridges: B:R.76, B:H.146, B:R.153, B:R.153, B:K.154, A:R.20, A:R.88 AH0-ALA-DGL-API-DAL-DAL.8: 22 residues within 4Å: Chain C: Y.26, T.27, A.28, L.29, A.37, R.76, W.78, H.79, A.80, G.81, V.82, N.90, N.92, E.99, H.146, R.153, K.154, D.156 Chain D: R.20, R.87, R.88, D.137 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:A.37, C:W.78 Hydrogen bonds: C:T.27, C:R.76, C:R.76, C:H.79, C:H.79, C:A.80, C:G.81, C:N.90, C:N.92 Salt bridges: C:R.76, C:H.146, C:R.153, C:K.154, C:K.154, D:R.20, D:R.87 AH0-ALA-DGL-API-DAL-DAL.9: 22 residues within 4Å: Chain C: R.20, R.88, D.137 Chain D: H.25, Y.26, T.27, A.28, L.29, A.37, A.43, R.76, W.78, H.79, A.80, G.81, N.90, N.92, E.99, H.146, R.153, K.154, D.156 18 PLIP interactions: 4 interactions with chain C, 14 interactions with chain D Hydrogen bonds: C:R.20, D:T.27, D:R.76, D:W.78, D:G.81, D:N.90, D:N.92 Water bridges: C:D.137 Salt bridges: C:R.20, C:R.88, D:R.76, D:H.146, D:R.153, D:R.153, D:K.154 Hydrophobic interactions: D:L.29, D:A.37, D:W.78

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

ACT.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ACT.4: 2 residues within 4Å: Chain B: S.8, Y.9 No protein-ligand interaction detected (PLIP) ACT.5: 3 residues within 4Å: Chain B: N.233, Y.234, D.235 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.234 Hydrogen bonds: B:Y.234 ACT.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ACT.11: 2 residues within 4Å: Chain D: S.8, Y.9 No protein-ligand interaction detected (PLIP) ACT.12: 3 residues within 4Å: Chain D: N.233, Y.234, D.235 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Y.234 Hydrogen bonds: D:Y.234, D:D.235

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 6 residues within 4Å: Chain A: Y.6 Chain B: K.17, R.134 Chain C: K.17, R.134, Y.135 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:K.17, B:K.17, B:R.134, C:R.134, C:R.134 PEG.7: 5 residues within 4Å: Chain B: P.52, H.53, K.58, K.63, G.64 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.63 PEG.13: 6 residues within 4Å: Chain A: K.17, R.134, Y.135 Chain C: Y.6 Chain D: K.17, R.134 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:R.134, A:R.134, D:K.17, D:K.17, D:R.134 PEG.14: 5 residues within 4Å: Chain D: P.52, H.53, K.58, K.63, G.64 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.63

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

AMPDH3

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