SMTL ID : 4f8b.1

Crystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase QueF

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-10-mer

Ligands

8 x GD1: 2-amino-5-[(Z)-iminomethyl]-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one(Covalent)(Non-covalent)

GD1.1: 12 residues within 4Å: Chain A: F.34, V.78, E.79, S.80 Chain B: C.56, P.57, K.58, D.63, F.96, H.97, E.98, I.131 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:V.78, A:E.79, A:S.80, B:H.97, B:H.97 Salt bridges: B:E.98 pi-Stacking: B:F.96, B:F.96 GD1.4: 11 residues within 4Å: Chain B: F.34, V.78, E.79, S.80 Chain C: C.56, P.57, D.63, F.96, H.97, E.98, I.131 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:F.96 Hydrogen bonds: C:H.97, C:H.97, B:V.78, B:E.79, B:S.80 Water bridges: C:D.63, C:E.98 Salt bridges: C:E.98 pi-Stacking: C:F.96 GD1.6: 11 residues within 4Å: Chain C: F.34, V.78, E.79, S.80 Chain D: C.56, P.57, D.63, F.96, H.97, E.98, I.131 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:V.78, C:E.79, C:S.80, D:H.97 Water bridges: D:E.98 Salt bridges: D:E.98 pi-Stacking: D:F.96, D:F.96 GD1.9: 12 residues within 4Å: Chain D: F.34, V.78, E.79, S.80 Chain E: C.56, P.57, K.58, D.63, F.96, H.97, E.98, I.131 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain E Hydrogen bonds: D:V.78, D:E.79, D:S.80, E:H.97 Water bridges: E:E.98 Salt bridges: E:E.98 pi-Stacking: E:F.96, E:F.96 GD1.11: 12 residues within 4Å: Chain F: F.34, V.78, E.79, S.80 Chain G: C.56, P.57, K.58, D.63, F.96, H.97, E.98, I.131 9 PLIP interactions: 4 interactions with chain F, 5 interactions with chain G Hydrogen bonds: F:V.78, F:E.79, F:E.79, F:S.80, G:H.97, G:H.97 Salt bridges: G:E.98 pi-Stacking: G:F.96, G:F.96 GD1.14: 11 residues within 4Å: Chain G: F.34, V.78, E.79, S.80 Chain H: C.56, P.57, D.63, F.96, H.97, E.98, I.131 10 PLIP interactions: 6 interactions with chain H, 4 interactions with chain G Hydrophobic interactions: H:F.96 Hydrogen bonds: H:H.97, H:H.97, G:V.78, G:E.79, G:E.79, G:S.80 Water bridges: H:H.97 Salt bridges: H:E.98 pi-Stacking: H:F.96 GD1.16: 11 residues within 4Å: Chain H: F.34, V.78, E.79, S.80 Chain I: C.56, P.57, D.63, F.96, H.97, E.98, I.131 8 PLIP interactions: 4 interactions with chain H, 4 interactions with chain I Hydrogen bonds: H:V.78, H:E.79, H:E.79, H:S.80, I:H.97 Salt bridges: I:E.98 pi-Stacking: I:F.96, I:F.96 GD1.19: 12 residues within 4Å: Chain I: F.34, V.78, E.79, S.80 Chain J: C.56, P.57, K.58, D.63, F.96, H.97, E.98, I.131 8 PLIP interactions: 4 interactions with chain I, 4 interactions with chain J Hydrogen bonds: I:V.78, I:E.79, I:E.79, I:S.80, J:H.97 Salt bridges: J:E.98 pi-Stacking: J:F.96, J:F.96

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain B: D.163, R.165 Chain J: R.165 Ligands: MG.20 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.163, H2O.2, H2O.2, H2O.12 MG.5: 4 residues within 4Å: Chain C: D.163, R.165 Chain I: R.165 Ligands: MG.17 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain I, 3 Ligand-Water interactions Metal complexes: C:D.163, I:R.165, H2O.3, H2O.3, H2O.11 MG.7: 4 residues within 4Å: Chain D: D.163, R.165 Chain H: R.165 Ligands: MG.15 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain H, 3 Ligand-Water interactions Metal complexes: D:D.163, H:R.165, H2O.5, H2O.5, H2O.5 MG.10: 4 residues within 4Å: Chain E: D.163, R.165 Chain G: R.165 Ligands: MG.12 5 PLIP interactions: 1 interactions with chain G, 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: G:R.165, E:D.163, H2O.6, H2O.6, H2O.6 MG.12: 4 residues within 4Å: Chain E: R.165 Chain G: D.163, R.165 Ligands: MG.10 4 PLIP interactions: 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:D.163, H2O.6, H2O.8, H2O.8 MG.15: 4 residues within 4Å: Chain D: R.165 Chain H: D.163, R.165 Ligands: MG.7 5 PLIP interactions: 1 interactions with chain H, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: H:D.163, D:R.165, H2O.5, H2O.10, H2O.10 MG.17: 4 residues within 4Å: Chain C: R.165 Chain I: D.163, R.165 Ligands: MG.5 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain I, 3 Ligand-Water interactions Metal complexes: C:R.165, I:D.163, H2O.11, H2O.11, H2O.11 MG.20: 4 residues within 4Å: Chain B: R.165 Chain J: D.163, R.165 Ligands: MG.2 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain J, 3 Ligand-Water interactions Metal complexes: B:R.165, J:D.163, H2O.12, H2O.12, H2O.12

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 1 residues within 4Å: Chain B: N.40 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.40, B:N.40, B:N.40 PO4.13: 1 residues within 4Å: Chain G: N.40 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:N.40, G:N.40, G:N.40

2 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.8: 13 residues within 4Å: Chain B: Y.150, N.154, Y.158 Chain C: Y.150, N.154, Y.158 Chain D: Y.150, N.154, L.157, Y.158 Chain E: Y.150, N.154, Y.158 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:Y.150, D:Y.150 PE4.18: 13 residues within 4Å: Chain G: Y.150, N.154, Y.158 Chain H: Y.150, N.154, Y.158 Chain I: Y.150, N.154, L.157, Y.158 Chain J: Y.150, N.154, Y.158 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:Y.150, J:Y.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chikwana, V.M. et al., Structural basis of biological nitrile reduction. J.Biol.Chem. (2012)

Release Date

2012-07-11

Peptides

NADPH-dependent 7-cyano-7-deazaguanine reductase: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
A

G
B

H
C

I
D

J
E

NADPH-dependent 7-cyano-7-deazaguanine reductase