SMTL ID : 6zk5.1

Plant nucleoside hydrolase - ZmNRh3 enzyme in complex with forodesine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.23, D.28, N.52, L.138, D.255 Ligands: IMH.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.23, A:D.28, A:L.138, A:D.255, H2O.1 CA.5: 6 residues within 4Å: Chain B: D.23, D.28, N.52, L.138, D.255 Ligands: IMH.4 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.23, B:D.28, B:D.28, B:L.138, H2O.7

2 x IMH: 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL(Non-covalent)

IMH.2: 18 residues within 4Å: Chain A: D.27, D.28, N.52, A.92, V.95, H.96, L.138, L.164, N.173, E.179, A.180, N.181, Y.238, W.241, H.254, D.255 Chain B: K.294 Ligands: CA.1 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.52, A:N.173, A:N.173, A:E.179, A:A.180, A:N.181, A:Y.238, A:Y.238, A:D.255, B:K.294 Water bridges: B:K.294 IMH.4: 18 residues within 4Å: Chain A: K.294 Chain B: D.27, D.28, N.52, A.92, V.95, H.96, L.138, L.164, N.173, E.179, A.180, N.181, Y.238, W.241, H.254, D.255 Ligands: CA.5 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.52, B:N.173, B:N.173, B:E.179, B:A.180, B:N.181, B:Y.238, B:Y.238, B:D.255, A:K.294 Water bridges: B:N.173, B:Y.246 pi-Stacking: B:H.96

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

EDO.3: 6 residues within 4Å: Chain A: E.266, L.267, F.268, T.313, V.314, D.315 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.266, A:V.314 EDO.7: 5 residues within 4Å: Chain B: S.16, K.160, L.262, V.263 Ligands: PGE.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.16, B:K.160, B:K.160

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

PGE.6: 8 residues within 4Å: Chain B: K.159, K.160, V.162, Y.200, A.261, L.262, P.265 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luptakova, E. et al., Plant nucleoside N-ribohydrolases: riboside binding and role in nitrogen storage mobilization. Plant J. (2023)

Release Date

2022-01-12

Peptides

Nucleoside N-ribohydrolase 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nucleoside N-ribohydrolase 3

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