SMTL ID : 4am8.2 (1 other biounit)

Crystal structure of the R54G mutant of putrescine transcarbamylase from Enterococcus faecalis bound to a curing guanidinium ion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-trimer

Ligands

3 x PAO: N-(PHOSPHONOACETYL)-L-ORNITHINE(Non-covalent)

PAO.1: 16 residues within 4Å: Chain A: S.52, T.53, G.54, T.55, R.103, M.125, H.130, Q.133, T.163, Q.164, V.165, D.227, C.269, L.270, R.297 Ligands: GAI.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.165 Hydrogen bonds: A:T.53, A:G.54, A:T.55, A:T.55, A:T.55, A:R.103, A:R.103, A:T.163, A:Q.164, A:Q.164, A:D.227, A:L.270, A:R.297 PAO.5: 16 residues within 4Å: Chain B: S.52, T.53, G.54, T.55, R.103, M.125, H.130, Q.133, T.163, Q.164, V.165, D.227, C.269, L.270, R.297 Ligands: GAI.6 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.165 Hydrogen bonds: B:T.53, B:G.54, B:T.55, B:T.55, B:R.103, B:R.103, B:Q.164, B:Q.164, B:D.227, B:L.270, B:R.297 PAO.8: 16 residues within 4Å: Chain C: S.52, T.53, G.54, T.55, R.103, M.125, H.130, T.163, Q.164, V.165, D.227, C.269, L.270, R.297 Ligands: GAI.3, GAI.9 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:V.165 Hydrogen bonds: C:T.53, C:G.54, C:T.55, C:T.55, C:R.103, C:R.103, C:Q.164, C:Q.164, C:D.227, C:L.270, C:R.297 Water bridges: C:T.53, C:T.53

4 x GAI: GUANIDINE(Non-covalent)

GAI.2: 6 residues within 4Å: Chain A: Q.50, S.51, R.103, M.125, Y.233 Ligands: PAO.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.51, A:R.103 Water bridges: A:Q.50 GAI.3: 6 residues within 4Å: Chain A: E.84, V.92 Chain C: G.54, L.270, P.271 Ligands: PAO.8 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain C Salt bridges: A:E.84 Hydrogen bonds: C:G.54 Water bridges: C:T.53, C:T.53, C:C.269 GAI.6: 6 residues within 4Å: Chain B: Q.50, S.51, R.103, M.125, Y.233 Ligands: PAO.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.50, B:Q.50, B:S.51, B:R.103 GAI.9: 6 residues within 4Å: Chain C: Q.50, S.51, R.103, M.125, Y.233 Ligands: PAO.8 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.50, C:S.51, C:S.51, C:R.103

1 x GLN: GLUTAMINE(Covalent)

GLN.4: 3 residues within 4Å: Chain A: Y.18 Chain B: F.333, T.336 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.18

1 x NI: NICKEL (II) ION(Non-covalent)

NI.7: 3 residues within 4Å: Chain A: H.69 Chain B: H.69 Chain C: H.69 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.69, C:H.69, B:H.69, H2O.1, H2O.8, H2O.11

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.10: 5 residues within 4Å: Chain C: D.161, A.162, F.188, G.231, L.232 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.161, C:D.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Polo, L.M. et al., Curing a Mutant Transcarbamylase with a Small Molecule: A Crystallographic View. To be Published

Release Date

2013-03-27

Peptides

PUTRESCINE CARBAMOYLTRANSFERASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

PUTRESCINE CARBAMOYLTRANSFERASE

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