SMTL ID : 5h8i.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-octamer

Ligands

16 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: 9 residues within 4Å: Chain A: R.286, R.287, P.288, D.289 Chain B: L.297 Chain C: P.141, G.142, D.143 Chain D: R.287 Ligand excluded by PLIP GOL.4: 5 residues within 4Å: Chain A: L.214, M.276, W.280 Chain B: S.198, H.201 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain B: V.25, S.26, P.77, T.78, R.81 Ligand excluded by PLIP GOL.6: 4 residues within 4Å: Chain B: E.54, G.55, F.58, R.69 Ligand excluded by PLIP GOL.7: 9 residues within 4Å: Chain A: R.287 Chain B: P.141, G.142, D.143 Chain C: L.297, V.303 Chain D: R.286, P.288, D.289 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: M.276, W.280 Chain D: I.196, S.198, H.201 Ligand excluded by PLIP GOL.13: 5 residues within 4Å: Chain C: V.25, S.26, P.77, T.78, R.81 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain D: V.25, S.26, P.77, T.78, R.81 Ligand excluded by PLIP GOL.20: 6 residues within 4Å: Chain E: I.196, S.198, H.201 Chain F: L.214, M.276, W.280 Ligand excluded by PLIP GOL.21: 5 residues within 4Å: Chain E: V.25, S.26, P.77, T.78, R.81 Ligand excluded by PLIP GOL.23: 4 residues within 4Å: Chain E: M.276, W.280 Chain F: S.198, H.201 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain F: V.25, S.26, P.77, T.78, R.81 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain F: Q.83, K.84, K.87, D.115, G.116 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain G: S.198, H.201 Chain H: L.214, M.276, W.280 Ligand excluded by PLIP

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

N2H.3: 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 9 PLIP interactions: 9 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 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 9 PLIP interactions: 9 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 N2H.15: 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 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:Y.133, D:Y.133, D:W.162, 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.19: 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 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:Y.133, E:Y.133, 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.22: 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 12 PLIP interactions: 12 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 Water bridges: F:C.161 N2H.27: 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 11 PLIP interactions: 11 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

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

PEG.8: 2 residues within 4Å: Chain B: I.252, I.255 No protein-ligand interaction detected (PLIP) PEG.17: 6 residues within 4Å: Chain D: Q.83, K.84, K.87, D.115, G.116, T.117 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.117

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

PGE.9: 7 residues within 4Å: Chain A: D.298 Chain B: A.174, L.175, Q.176, G.177, R.277, F.283 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.298, B:R.277 Water bridges: B:R.277

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

EDO.14: 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.26: 5 residues within 4Å: Chain D: P.141 Chain E: V.303 Chain F: R.286, P.288, D.289 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain F Water bridges: C:R.287, C:R.287, C:D.289, F:R.287 Hydrogen bonds: F:D.289 EDO.29: 6 residues within 4Å: Chain F: P.141 Chain G: V.303 Chain H: R.286, R.287, P.288, D.289 6 PLIP interactions: 2 interactions with chain H, 4 interactions with chain E Hydrogen bonds: H:D.289 Water bridges: H:R.287, E:R.287, E:R.287, E:R.287, E:D.289

1 x NA: SODIUM ION(Non-functional Binders)

NA.18: 1 residues within 4Å: Chain D: V.263 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.263

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
I

B
J

C
K

D
L

E
M

F
N

G
O

H
P

N-carbamoylputrescine amidohydrolase

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