SMTL ID : 5h8l.1 (1 other biounit)

Crystal structure of Medicago truncatula N-carbamoylputrescine amidohydrolase (MtCPA) C158S mutant in complex with putrescine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-octamer

Ligands

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: V.25, S.26, T.78, R.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.78, A:R.81 GOL.2: 5 residues within 4Å: Chain A: Y.57, Q.60, A.186, I.187, G.188 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.57, A:G.188, A:G.188 GOL.5: 4 residues within 4Å: Chain A: M.276, W.280 Chain B: S.198, H.201 No protein-ligand interaction detected (PLIP) GOL.6: 4 residues within 4Å: Chain B: E.54, F.58, R.69, K.71 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.69 Water bridges: B:E.54, B:G.55, B:Y.56, B:F.98 GOL.10: 6 residues within 4Å: Chain C: L.214, M.276, W.280 Chain D: I.196, S.198, H.201 No protein-ligand interaction detected (PLIP) GOL.11: 5 residues within 4Å: Chain C: V.25, S.26, P.77, T.78, R.81 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.78, C:R.81 GOL.13: 5 residues within 4Å: Chain C: I.196, S.198, H.201 Chain D: M.276, W.280 No protein-ligand interaction detected (PLIP) GOL.15: 4 residues within 4Å: Chain C: R.204 Chain D: Q.207, E.251, I.252 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Q.207, D:I.252, C:R.204 Water bridges: D:Q.207, C:Q.207, C:Q.207 GOL.20: 4 residues within 4Å: Chain E: S.198, H.201 Chain F: M.276, W.280 1 PLIP interactions: 1 interactions with chain E Water bridges: E:S.195 GOL.21: 5 residues within 4Å: Chain E: M.276, W.280 Chain F: I.196, S.198, H.201 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:H.201 GOL.22: 5 residues within 4Å: Chain E: V.25, S.26, P.77, T.78, R.81 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.26, E:T.78, E:R.81 GOL.23: 3 residues within 4Å: Chain E: Q.83, D.115, G.116 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.83 Water bridges: E:K.87 GOL.25: 5 residues within 4Å: Chain F: V.25, S.26, P.77, T.78, R.81 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:T.78, F:T.78, F:R.81 GOL.29: 5 residues within 4Å: Chain G: I.196, S.198, H.201 Chain H: M.276, W.280 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:H.201, H:M.276 GOL.30: 2 residues within 4Å: Chain G: K.259, E.260 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:E.260

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

EDO.3: 4 residues within 4Å: Chain A: R.286, P.288, D.289 Chain B: V.303 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Water bridges: D:R.287, D:D.289 Hydrogen bonds: A:D.289, A:D.289 EDO.7: 2 residues within 4Å: Chain B: I.252, I.255 No protein-ligand interaction detected (PLIP) EDO.8: 4 residues within 4Å: Chain A: R.204 Chain B: Q.207, E.251, I.252 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:R.204, B:Q.207 Hydrogen bonds: B:Q.207, B:I.252 EDO.12: 5 residues within 4Å: Chain C: R.287, P.288, D.289 Chain D: V.303 Chain E: P.141 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:D.289 Water bridges: F:R.287 EDO.16: 5 residues within 4Å: Chain B: P.141 Chain C: V.303 Chain D: R.286, P.288, D.289 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:D.289 Water bridges: D:R.287, A:R.287, A:R.287 EDO.17: 1 residues within 4Å: Chain D: H.192 1 PLIP interactions: 1 interactions with chain D Water bridges: D:Q.194 EDO.26: 5 residues within 4Å: Chain D: P.141 Chain E: V.303 Chain F: R.286, P.288, D.289 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain C Hydrogen bonds: F:D.289 Water bridges: C:D.289, C:D.289 EDO.27: 3 residues within 4Å: Chain F: S.26, T.27, T.30 1 PLIP interactions: 1 interactions with chain F Water bridges: F:T.27

6 x PUT: 1,4-DIAMINOBUTANE(Non-covalent)

PUT.4: 8 residues within 4Å: Chain A: W.280 Chain B: P.128, Y.133, S.161, W.162, A.186, I.187, E.190 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.133, B:Y.133, B:W.162, B:I.187 Hydrogen bonds: B:S.161, B:S.161, B:E.190 Water bridges: B:W.162 PUT.9: 7 residues within 4Å: Chain C: Y.133, S.161, W.162, A.186, I.187, E.190 Chain D: W.280 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:Y.133, C:Y.133, C:W.162, C:I.187 Hydrogen bonds: C:S.161, C:S.161, C:E.190 Water bridges: C:W.162 PUT.14: 8 residues within 4Å: Chain C: W.280 Chain D: P.128, Y.133, S.161, W.162, A.186, I.187, E.190 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:Y.133, D:Y.133, D:W.162, D:I.187 Hydrogen bonds: D:S.161, D:S.161, D:E.190 Water bridges: D:W.162 PUT.19: 7 residues within 4Å: Chain E: Y.133, S.161, W.162, A.186, I.187, E.190 Chain F: W.280 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:Y.133, E:Y.133, E:W.162, E:I.187 Hydrogen bonds: E:S.161, E:E.190 Water bridges: E:W.162 PUT.24: 7 residues within 4Å: Chain E: W.280 Chain F: Y.133, S.161, W.162, A.186, I.187, E.190 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:Y.133, F:Y.133, F:W.162, F:I.187 Hydrogen bonds: F:S.161, F:S.161, F:E.190 Water bridges: F:W.162 PUT.28: 8 residues within 4Å: Chain G: P.128, Y.133, S.161, W.162, A.186, I.187, E.190 Chain H: W.280 9 PLIP interactions: 9 interactions with chain G Hydrophobic interactions: G:Y.133, G:Y.133, G:W.162, G:W.162, G:I.187 Hydrogen bonds: G:S.161, G:S.161, G:E.190 Water bridges: G:W.162

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

PEG.18: 6 residues within 4Å: Chain D: Q.83, K.84, K.87, D.115, G.116, T.117 No protein-ligand interaction detected (PLIP)

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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