SMTL ID : 4am8.1 (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

2 x GLN: GLUTAMINE(Covalent)

GLN.1: 4 residues within 4Å: Chain A: F.333, D.335, T.336 Chain C: Y.18 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.333 Hydrogen bonds: A:F.333 GLN.10: 4 residues within 4Å: Chain B: Y.18 Chain C: F.333, D.335, T.336 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.333 Hydrogen bonds: C:F.333, C:T.336

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

PAO.2: 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.3 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.7: 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.8 14 PLIP interactions: 14 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 Water bridges: B:T.53, B:T.53 PAO.11: 15 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.12 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:V.165 Hydrogen bonds: C:T.53, C:G.54, C:T.55, 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

3 x GAI: GUANIDINE(Non-covalent)

GAI.3: 6 residues within 4Å: Chain A: Q.50, S.51, R.103, M.125, Y.233 Ligands: PAO.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.51, A:S.51, A:R.103 GAI.8: 6 residues within 4Å: Chain B: Q.50, S.51, R.103, M.125, Y.233 Ligands: PAO.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.50, B:Q.50, B:S.51, B:R.103 GAI.12: 6 residues within 4Å: Chain C: Q.50, S.51, R.103, M.125, Y.233 Ligands: PAO.11 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.50, C:Q.50, C:S.51, C:R.103

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

TRS.4: 5 residues within 4Å: Chain A: D.161, A.162, F.188, G.231, L.232 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.127, A:G.231 TRS.9: 5 residues within 4Å: Chain B: D.161, A.162, F.188, G.231, L.232 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.161 Water bridges: B:D.127, B:D.127, B:D.161, B:D.161, B:A.162 TRS.13: 4 residues within 4Å: Chain C: D.161, A.162, F.188, G.231 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:D.161 Water bridges: C:D.127, C:D.161, C:A.162, C:A.162, C:Q.164, C:G.231

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

NI.5: 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 B, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: A:H.69, B:H.69, C:H.69, H2O.3, H2O.9, H2O.15

1 x ILE: ISOLEUCINE(Covalent)

ILE.6: 3 residues within 4Å: Chain A: Y.18, Y.307 Chain B: S.338 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.307

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
A

B
B

C
C

PUTRESCINE CARBAMOYLTRANSFERASE

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