SMTL ID : 5udg.1

Mutant E97Q crystal structure of Bacillus subtilis QueF with a disulfide Cys 55-99

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-10-mer

Ligands

14 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.143, R.145 Chain I: R.145 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain I, 2 Ligand-Water interactions Metal complexes: A:D.143, I:R.145, H2O.2, H2O.19 MG.2: 2 residues within 4Å: Chain A: D.87, E.90 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.87, A:E.90, H2O.2 MG.4: 3 residues within 4Å: Chain B: R.145 Chain H: D.143, R.145 2 PLIP interactions: 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.143, H2O.5 MG.7: 2 residues within 4Å: Chain D: D.54, E.55 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.54, D:E.55, H2O.7, H2O.7, H2O.8 MG.8: 4 residues within 4Å: Chain D: T.141, D.143, R.145 Chain F: R.145 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: F:R.145, D:D.143, H2O.8 MG.10: 2 residues within 4Å: Chain E: D.143, R.145 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.143, E:D.143, H2O.10 MG.11: 3 residues within 4Å: Chain E: D.54, E.55, K.119 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.54, E:E.55, H2O.9, H2O.10 MG.12: 3 residues within 4Å: Chain D: R.145 Chain F: D.143, R.145 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: D:R.145, F:D.143, H2O.8, H2O.13 MG.13: 2 residues within 4Å: Chain F: D.87, E.90 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.87, F:E.90, H2O.13 MG.15: 3 residues within 4Å: Chain C: D.143, R.145 Chain G: R.145 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.143, H2O.16 MG.18: 2 residues within 4Å: Chain I: D.54, E.55 5 PLIP interactions: 2 interactions with chain I, 3 Ligand-Water interactions Metal complexes: I:D.54, I:E.55, H2O.18, H2O.18, H2O.19 MG.19: 4 residues within 4Å: Chain A: R.145 Chain I: T.141, D.143, R.145 3 PLIP interactions: 1 interactions with chain I, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: I:D.143, A:R.145, H2O.19 MG.21: 2 residues within 4Å: Chain J: D.143, R.145 3 PLIP interactions: 2 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:D.143, J:D.143, H2O.21 MG.22: 3 residues within 4Å: Chain J: D.54, E.55, K.119 4 PLIP interactions: 2 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:D.54, J:E.55, H2O.20, H2O.21

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

PGE.3: 3 residues within 4Å: Chain A: G.121, T.122, K.123 No protein-ligand interaction detected (PLIP) PGE.5: 7 residues within 4Å: Chain B: V.19, N.20, R.21, D.22, R.95, K.123, Y.124 No protein-ligand interaction detected (PLIP) PGE.6: 7 residues within 4Å: Chain C: K.64, L.65, F.68 Chain D: G.107 Chain F: Q.41, P.42, R.106 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.64 PGE.9: 6 residues within 4Å: Chain D: V.19, N.20, R.21, D.22, R.95, K.123 1 PLIP interactions: 1 interactions with chain D Water bridges: D:D.22 PGE.14: 3 residues within 4Å: Chain F: G.121, T.122, K.123 No protein-ligand interaction detected (PLIP) PGE.16: 7 residues within 4Å: Chain G: V.19, N.20, R.21, D.22, R.95, K.123, Y.124 No protein-ligand interaction detected (PLIP) PGE.17: 7 residues within 4Å: Chain A: Q.41, P.42, R.106 Chain H: K.64, L.65, F.68 Chain I: G.107 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:K.64 PGE.20: 6 residues within 4Å: Chain I: V.19, N.20, R.21, D.22, R.95, K.123 1 PLIP interactions: 1 interactions with chain I Water bridges: I:D.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mohammad, A. et al., Protection of the Queuosine Biosynthesis Enzyme QueF from Irreversible Oxidation by a Conserved Intramolecular Disulfide. Biomolecules (2017)

Release Date

2017-03-29

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