SMTL ID : 4a8h.1 (1 other biounit)

Crystal structure of putrescine transcarbamylase from Enterococcus faecalis with N-(phosphonoacetyl)-putrescine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

3 x PUW: N-(PHOSPHONOACETYL)-PUTRESCINE(Non-covalent)

PUW.1: 17 residues within 4Å: Chain A: S.52, T.53, R.54, T.55, R.103, M.125, H.130, Q.133, T.163, Q.164, V.165, D.227, Y.233, C.269, L.270, R.297 Chain C: Q.79 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.165 Hydrogen bonds: A:S.52, A:T.53, A:R.54, A:R.54, A:T.55, A:T.55, A:R.103, A:R.103, A:Q.133, A:D.227, A:L.270, A:R.297, C:Q.79 Water bridges: A:Q.164, A:Q.164 PUW.7: 17 residues within 4Å: Chain A: Q.79 Chain B: S.52, T.53, R.54, T.55, R.103, M.125, H.130, Q.133, T.163, Q.164, V.165, D.227, Y.233, C.269, L.270, R.297 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.165 Hydrogen bonds: B:S.52, B:T.53, B:R.54, B:R.54, B:T.55, B:T.55, B:R.103, B:R.103, B:Q.133, B:D.227, B:L.270, B:R.297, A:Q.79 Water bridges: B:Q.164, B:Q.164 PUW.13: 17 residues within 4Å: Chain B: Q.79 Chain C: S.52, T.53, R.54, T.55, R.103, M.125, H.130, Q.133, T.163, Q.164, V.165, D.227, Y.233, C.269, L.270, R.297 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.165 Hydrogen bonds: C:S.52, C:T.53, C:R.54, C:R.54, C:T.55, C:T.55, C:R.103, C:R.103, C:Q.133, C:D.227, C:L.270, C:R.297, B:Q.79 Water bridges: C:Q.164, C:Q.164

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

TRS.2: 5 residues within 4Å: Chain A: D.161, A.162, F.188, G.231, L.232 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.161 Water bridges: A:D.127, A:D.161, A:D.161, A:D.161, A:Q.164, A:G.231 TRS.8: 5 residues within 4Å: Chain B: D.161, A.162, F.188, G.231, L.232 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.161 Water bridges: B:D.127, B:D.161, B:D.161, B:D.161, B:Q.164, B:G.231 TRS.14: 5 residues within 4Å: Chain C: D.161, A.162, F.188, G.231, L.232 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:D.161 Water bridges: C:D.127, C:D.161, C:D.161, C:D.161, C:Q.164, C:G.231

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: R.91, R.95 Chain B: F.291 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.91, A:R.95 SO4.9: 3 residues within 4Å: Chain B: R.91, R.95 Chain C: F.291 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.91, B:R.95 SO4.15: 3 residues within 4Å: Chain A: F.291 Chain C: R.91, R.95 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.91, C:R.95

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 3 residues within 4Å: Chain A: N.41, G.67 Chain B: E.64 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.64 EDO.5: 2 residues within 4Å: Chain A: G.261, A.262 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.262 Water bridges: A:D.258, A:D.258, A:N.263 EDO.10: 3 residues within 4Å: Chain B: N.41, G.67 Chain C: E.64 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.64 EDO.11: 2 residues within 4Å: Chain B: G.261, A.262 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.262 Water bridges: B:D.258, B:D.258, B:N.263 EDO.16: 3 residues within 4Å: Chain A: E.64 Chain C: N.41, G.67 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.64 EDO.17: 2 residues within 4Å: Chain C: G.261, A.262 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.262 Water bridges: C:D.258, C:D.258, C:N.263

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

NI.6: 5 residues within 4Å: Chain A: H.69 Chain B: H.69 Chain C: H.69 Ligands: NI.12, NI.18 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.2, H2O.9, H2O.15 NI.12: 5 residues within 4Å: Chain A: H.69 Chain B: H.69 Chain C: H.69 Ligands: NI.6, NI.18 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.2, H2O.9, H2O.15 NI.18: 5 residues within 4Å: Chain A: H.69 Chain B: H.69 Chain C: H.69 Ligands: NI.6, NI.12 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: C:H.69, A:H.69, B:H.69, H2O.2, H2O.9, H2O.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Polo, L.M. et al., New Insight Into the Transcarbamylase Family: The Structure of Putrescine Transcarbamylase, a Key Catalyst for Fermentative Utilization of Agmatine. Plos One (2012)

Release Date

2012-02-15

Peptides

PUTRESCINE CARBAMOYLTRANSFERASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

PUTRESCINE CARBAMOYLTRANSFERASE

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