SMTL ID : 5h8i.1 (1 other biounit)

Crystal structure of Medicago truncatula N-carbamoylputrescine amidohydrolase (MtCPA) in complex with N-(dihydroxymethyl)putrescine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-octamer

Ligands

19 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: S.26, P.77, T.78, R.81 Ligand excluded by PLIP GOL.2: 1 residues within 4Å: Chain A: N.140 Ligand excluded by PLIP GOL.3: 4 residues within 4Å: Chain A: Y.57, A.186, I.187, G.188 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: M.276, W.280 Chain B: S.198, H.201 Ligand excluded by PLIP GOL.9: 4 residues within 4Å: Chain B: E.54, F.58, R.69, F.98 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain C: I.196, S.198, H.201 Chain D: M.276, W.280 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain C: V.25, S.26, P.77, T.78, R.81 Ligand excluded by PLIP GOL.13: 5 residues within 4Å: Chain C: E.54, G.55, F.58, R.69, F.98 Ligand excluded by PLIP GOL.14: 4 residues within 4Å: Chain C: R.204 Chain D: Q.207, E.251, I.252 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain C: M.276, W.280 Chain D: I.196, S.198, H.201 Ligand excluded by PLIP GOL.19: 5 residues within 4Å: Chain D: V.25, S.26, P.77, T.78, R.81 Ligand excluded by PLIP GOL.24: 4 residues within 4Å: Chain E: S.198, H.201 Chain F: M.276, W.280 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain E: M.276, W.280 Chain F: I.196, S.198, H.201 Ligand excluded by PLIP GOL.26: 5 residues within 4Å: Chain E: V.25, S.26, P.77, T.78, R.81 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain E: Q.83, K.84, K.87, D.115, G.116 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain F: V.25, S.26, P.77, T.78, R.81 Ligand excluded by PLIP GOL.30: 8 residues within 4Å: Chain C: R.287 Chain D: P.141, G.142 Chain E: L.297 Chain F: R.286, R.287, P.288, D.289 Ligand excluded by PLIP GOL.32: 2 residues within 4Å: Chain G: K.259, E.260 Ligand excluded by PLIP GOL.35: 6 residues within 4Å: Chain G: I.196, S.198, H.201 Chain H: L.214, M.276, W.280 Ligand excluded by PLIP

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

PEG.4: 4 residues within 4Å: Chain A: K.84, K.87, D.115, G.116 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.115 PEG.20: 5 residues within 4Å: Chain D: Q.83, K.84, D.115, G.116, T.117 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.83, D:Q.83, D:T.117 PEG.21: 3 residues within 4Å: Chain D: K.259, E.260, E.261 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.259, D:K.259, D:E.261 PEG.33: 2 residues within 4Å: Chain G: E.33, R.81 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:E.33

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 7 residues within 4Å: Chain A: D.298, K.300 Chain B: L.175, Q.176, G.177, R.277, F.283 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.277, A:K.300 Water bridges: B:R.277 PGE.15: 6 residues within 4Å: Chain C: Q.83, K.84, K.87, D.115, G.116, T.117 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.87 Water bridges: C:K.87 PGE.34: 3 residues within 4Å: Chain G: R.10, Q.150, K.155 No protein-ligand interaction detected (PLIP)

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

EDO.6: 6 residues within 4Å: Chain A: R.286, R.287, P.288, D.289 Chain B: V.303 Chain C: P.141 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Water bridges: D:R.287 Hydrogen bonds: A:D.289 EDO.16: 5 residues within 4Å: Chain C: R.286, P.288, D.289 Chain D: V.303 Chain E: P.141 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:D.289 Water bridges: C:R.287, F:R.287, F:R.287 EDO.22: 5 residues within 4Å: Chain B: P.141 Chain C: V.303 Chain D: R.286, P.288, D.289 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: D:D.289 Water bridges: D:R.287, A:R.287, A:R.287, C:L.304

6 x N2H: (4-azanylbutylamino)methanediol(Covalent)

N2H.7: 12 residues within 4Å: Chain A: W.280 Chain B: E.51, Y.57, K.124, P.128, Y.133, E.135, C.161, W.162, A.186, I.187, E.190 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.133, B:Y.133, B:W.162, B:I.187 Hydrogen bonds: B:K.124, B:W.162, B:A.186, B:A.186, B:E.190 Water bridges: B:C.161, B:Q.164 N2H.10: 12 residues within 4Å: Chain C: E.51, Y.57, K.124, P.128, Y.133, E.135, C.161, W.162, A.186, I.187, E.190 Chain D: W.280 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Y.133, C:Y.133, C:W.162, C:I.187 Hydrogen bonds: C:K.124, C:W.162, C:A.186, C:A.186, C:E.190 Water bridges: C:C.161 N2H.17: 12 residues within 4Å: Chain C: W.280 Chain D: E.51, Y.57, K.124, P.128, Y.133, E.135, C.161, W.162, A.186, I.187, E.190 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:Y.133, D:Y.133, D:W.162, D:I.187 Hydrogen bonds: D:K.124, D:W.162, D:A.186, D:A.186, D:E.190 Water bridges: D:C.161 N2H.23: 12 residues within 4Å: Chain E: E.51, Y.57, K.124, P.128, Y.133, E.135, C.161, W.162, A.186, I.187, E.190 Chain F: W.280 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:Y.133, E:Y.133, E:W.162, E:W.162, E:I.187 Hydrogen bonds: E:K.124, E:W.162, E:A.186, E:A.186, E:E.190 Water bridges: E:C.161 N2H.28: 12 residues within 4Å: Chain E: W.280 Chain F: E.51, Y.57, K.124, P.128, Y.133, E.135, C.161, W.162, A.186, I.187, E.190 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:Y.133, F:Y.133, F:W.162, F:W.162, F:I.187 Hydrogen bonds: F:Y.57, F:K.124, F:W.162, F:A.186, F:A.186, F:E.190 N2H.31: 12 residues within 4Å: Chain G: E.51, Y.57, K.124, P.128, Y.133, E.135, C.161, W.162, A.186, I.187, E.190 Chain H: W.280 12 PLIP interactions: 12 interactions with chain G Hydrophobic interactions: G:Y.133, G:Y.133, G:W.162, G:I.187 Hydrogen bonds: G:Y.57, G:K.124, G:W.162, G:A.186, G:A.186, G:E.190 Water bridges: G:C.161, G:Q.164

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sekula, B. et al., Structural Investigations of N-carbamoylputrescine Amidohydrolase from Medicago truncatula: Insights into the Ultimate Step of Putrescine Biosynthesis in Plants. Front Plant Sci (2016)

Release Date

2016-04-20

Peptides

N-carbamoylputrescine amidohydrolase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

N-carbamoylputrescine amidohydrolase

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