SMTL ID : 5h8j.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-octamer

Ligands

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: L.214, M.276, W.280 Chain B: S.198, H.201 No protein-ligand interaction detected (PLIP) GOL.2: 5 residues within 4Å: Chain A: V.25, S.26, P.77, T.78, R.81 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.26, A:T.78, A:R.81 GOL.3: 8 residues within 4Å: Chain A: Y.57, Q.60, Y.133, A.186, I.187, G.188, S.189, I.237 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.57, A:G.188 Water bridges: A:E.190, A:E.190 GOL.8: 5 residues within 4Å: Chain C: I.196, S.198, H.201 Chain D: M.276, W.280 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.201 GOL.9: 5 residues within 4Å: Chain C: M.276, W.280 Chain D: I.196, S.198, H.201 No protein-ligand interaction detected (PLIP) GOL.15: 5 residues within 4Å: Chain E: I.196, S.198, H.201 Chain F: M.276, W.280 2 PLIP interactions: 2 interactions with chain E Water bridges: E:D.197, E:H.201 GOL.16: 5 residues within 4Å: Chain E: M.276, W.280 Chain F: I.196, S.198, H.201 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:H.201, E:M.276 Water bridges: F:D.197 GOL.17: 5 residues within 4Å: Chain E: V.25, S.26, P.77, T.78, R.81 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.78, E:R.81 Water bridges: E:V.25, E:S.26 GOL.19: 4 residues within 4Å: Chain F: S.26, P.77, T.78, R.81 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:T.78, F:T.78, F:R.81 Water bridges: F:S.26 GOL.22: 5 residues within 4Å: Chain G: S.198, H.201 Chain H: L.214, M.276, W.280 6 PLIP interactions: 1 interactions with chain H, 5 interactions with chain G Water bridges: H:M.276, G:D.197, G:D.197, G:D.197, G:H.201 Hydrogen bonds: G:H.201 GOL.23: 5 residues within 4Å: Chain G: V.25, S.26, P.77, T.78, R.81 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:T.78, G:R.81

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

EDO.4: 5 residues within 4Å: Chain A: R.286, P.288, D.289 Chain B: V.303 Chain C: P.141 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Water bridges: D:R.287, D:D.289, A:R.287, A:R.287 Hydrogen bonds: A:D.289 EDO.6: 3 residues within 4Å: Chain B: A.174, R.277, F.283 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.277 Water bridges: B:R.277 EDO.10: 5 residues within 4Å: Chain C: R.286, P.288, D.289 Chain D: V.303 Chain E: P.141 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain C Water bridges: F:R.287, F:R.287, F:R.287, F:R.287, F:D.289 Hydrogen bonds: C:R.286 EDO.13: 5 residues within 4Å: Chain B: P.141 Chain C: V.303 Chain D: R.286, P.288, D.289 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Water bridges: A:R.287, A:R.287, A:R.287, D:R.287 EDO.20: 5 residues within 4Å: Chain D: P.141 Chain E: V.303 Chain F: R.286, P.288, D.289 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain C Hydrogen bonds: F:D.289, C:D.289 Water bridges: F:R.287, F:R.287, C:R.287, C:R.287

6 x N2P: PENTANE-1,5-DIAMINE(Non-covalent)

N2P.5: 11 residues within 4Å: Chain A: W.280 Chain B: E.51, Y.57, P.128, Y.133, E.135, C.161, W.162, A.186, I.187, E.190 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:P.128, B:Y.133, B:Y.133, B:W.162, B:W.162, B:I.187 Hydrogen bonds: B:E.51, B:E.190 N2P.7: 10 residues within 4Å: Chain C: Y.57, P.128, Y.133, E.135, C.161, W.162, A.186, I.187, E.190 Chain D: W.280 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:P.128, C:Y.133, C:W.162, C:W.162, C:I.187 Hydrogen bonds: C:E.51, C:E.190 N2P.11: 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 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:Y.133, D:Y.133, D:W.162, D:W.162, D:I.187 Hydrogen bonds: D:E.51, D:K.124, D:E.190 N2P.14: 11 residues within 4Å: Chain E: E.51, Y.57, P.128, Y.133, E.135, C.161, W.162, A.186, I.187, E.190 Chain F: W.280 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:P.128, E:Y.133, E:Y.133, E:W.162, E:I.187 Hydrogen bonds: E:E.51, E:K.124, E:E.190 N2P.18: 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 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:P.128, F:Y.133, F:Y.133, F:W.162, F:W.162, F:I.187 Hydrogen bonds: F:E.51, F:Y.57, F:K.124, F:E.190 N2P.21: 11 residues within 4Å: Chain G: E.51, Y.57, P.128, Y.133, E.135, C.161, W.162, A.186, I.187, E.190 Chain H: W.280 10 PLIP interactions: 10 interactions with chain G Hydrophobic interactions: G:P.128, G:Y.133, G:Y.133, G:W.162, G:W.162, G:I.187 Hydrogen bonds: G:E.51, G:Y.57, G:K.124, G:E.190

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

PEG.12: 6 residues within 4Å: Chain D: Q.83, K.84, K.87, D.115, G.116, T.117 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.115, D:T.117

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

Related Entries With Identical Sequence