SMTL ID : 5jyx.1 (1 other biounit)

Crystal structure of the covalent thioimide intermediate of the archaeosine synthase QueF-Like

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.74 Å

Oligo State

homo-10-mer

Ligands

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

GD1.1: 13 residues within 4Å: Chain A: C.21, I.23, D.28, L.61, H.62, E.63, Y.90 Chain G: L.2, V.42, L.43, A.44, I.45, E.46 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain G Hydrophobic interactions: A:L.61, G:I.45 Hydrogen bonds: A:H.62, G:L.43, G:I.45 Salt bridges: A:E.63 Water bridges: G:L.43 GD1.2: 12 residues within 4Å: Chain B: C.21, I.23, D.28, L.61, H.62, E.63, Y.90 Chain C: L.2, L.43, A.44, I.45, E.46 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:I.23, B:L.61, C:I.45 Hydrogen bonds: B:H.62, B:H.62, C:L.43, C:I.45 Water bridges: B:E.63 Salt bridges: B:E.63 GD1.4: 12 residues within 4Å: Chain C: C.21, I.23, D.28, L.61, H.62, E.63, Y.90 Chain J: L.2, L.43, A.44, I.45, E.46 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain J Hydrophobic interactions: C:Y.90, J:I.45 Hydrogen bonds: C:H.62, C:H.62, J:L.43, J:I.45 Salt bridges: C:E.63 GD1.5: 13 residues within 4Å: Chain A: L.2, V.42, L.43, A.44, I.45, E.46 Chain D: C.21, I.23, D.28, L.61, H.62, E.63, Y.90 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:L.61, A:I.45 Hydrogen bonds: D:H.62, D:H.62, A:L.43, A:I.45 Salt bridges: D:E.63 Water bridges: A:L.43 GD1.6: 13 residues within 4Å: Chain D: L.2, V.42, L.43, A.44, I.45, E.46 Chain E: C.21, I.23, D.28, L.61, H.62, E.63, Y.90 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:I.45, E:L.61 Hydrogen bonds: D:L.43, D:I.45, E:H.62 Water bridges: D:L.43 Salt bridges: E:E.63 GD1.7: 13 residues within 4Å: Chain B: L.2, V.42, L.43, A.44, I.45, E.46 Chain F: C.21, I.23, D.28, L.61, H.62, E.63, Y.90 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain F Hydrophobic interactions: B:I.45, F:L.61 Hydrogen bonds: B:L.43, B:I.45, F:H.62 Water bridges: B:L.43, F:D.28 Salt bridges: F:E.63 GD1.8: 12 residues within 4Å: Chain G: C.21, I.23, D.28, L.61, H.62, E.63, Y.90 Chain H: L.2, L.43, A.44, I.45, E.46 8 PLIP interactions: 3 interactions with chain H, 5 interactions with chain G Hydrophobic interactions: H:I.45, G:I.23, G:L.61 Hydrogen bonds: H:L.43, H:I.45, G:H.62, G:H.62 Salt bridges: G:E.63 GD1.10: 12 residues within 4Å: Chain E: L.2, L.43, A.44, I.45, E.46 Chain H: C.21, I.23, D.28, L.61, H.62, E.63, Y.90 7 PLIP interactions: 3 interactions with chain E, 4 interactions with chain H Hydrophobic interactions: E:I.45, H:Y.90 Hydrogen bonds: E:L.43, E:I.45, H:H.62, H:H.62 Salt bridges: H:E.63 GD1.11: 13 residues within 4Å: Chain F: L.2, V.42, L.43, A.44, I.45, E.46 Chain I: C.21, I.23, D.28, L.61, H.62, E.63, Y.90 8 PLIP interactions: 4 interactions with chain I, 4 interactions with chain F Hydrophobic interactions: I:L.61, F:I.45 Hydrogen bonds: I:H.62, F:L.43, F:I.45 Water bridges: I:D.28, F:L.43 Salt bridges: I:E.63 GD1.12: 13 residues within 4Å: Chain I: L.2, V.42, L.43, A.44, I.45, E.46 Chain J: C.21, I.23, D.28, L.61, H.62, E.63, Y.90 8 PLIP interactions: 4 interactions with chain I, 4 interactions with chain J Hydrophobic interactions: I:I.45, J:L.61 Hydrogen bonds: I:L.43, I:I.45, J:H.62 Water bridges: I:L.43, J:D.28 Salt bridges: J:E.63

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

NA.3: 5 residues within 4Å: Chain B: E.31, V.32, S.33, T.85, K.87 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.31, B:E.31, B:S.33 Water bridges: B:S.33 NA.9: 5 residues within 4Å: Chain G: E.31, V.32, S.33, T.85, K.87 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:S.33, G:S.33 Water bridges: G:S.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mei, X. et al., Crystal structure of the archaeosine synthase QueF-like-Insights into amidino transfer and tRNA recognition by the tunnel fold. Proteins (2017)

Release Date

2016-11-09

Peptides

Archeaosine synthase QueF-Like: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
J

D
M

E
N

F
A

G
C

H
J

I
M

J
N

Archeaosine synthase QueF-Like

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