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

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

Coordinates

PDB Format

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: 12 residues within 4Å: Chain A: 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 A, 3 interactions with chain C Hydrophobic interactions: A:L.61, A:Y.90 Hydrogen bonds: A:H.62, A:H.62, C:L.43, C:I.45 Water bridges: A:D.28, C:L.43 Salt bridges: A:E.63 GD1.2: 13 residues within 4Å: Chain B: C.21, I.23, D.28, L.61, H.62, E.63, Y.90 Chain F: L.2, V.42, L.43, A.44, I.45, E.46 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain F Hydrophobic interactions: B:I.23, B:L.61, F:I.45 Hydrogen bonds: B:H.62, B:H.62, F:L.43, F:I.45 Salt bridges: B:E.63 GD1.3: 12 residues within 4Å: Chain C: C.21, I.23, D.28, L.61, H.62, E.63, Y.90 Chain D: L.2, L.43, A.44, I.45, E.46 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:I.23, C:L.61, D:I.45 Hydrogen bonds: C:H.62, D:L.43, D:I.45 Water bridges: C:D.28, D:L.43 Salt bridges: C:E.63 GD1.5: 12 residues within 4Å: Chain D: C.21, P.22, I.23, D.28, L.61, H.62, E.63, Y.90 Chain J: L.43, A.44, I.45, E.46 8 PLIP interactions: 4 interactions with chain J, 4 interactions with chain D Hydrophobic interactions: J:I.45, D:L.61 Hydrogen bonds: J:L.43, J:I.45, D:H.62, D:H.62 Water bridges: J:L.43 Salt bridges: D:E.63 GD1.6: 12 residues within 4Å: Chain B: 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 8 PLIP interactions: 4 interactions with chain E, 4 interactions with chain B Hydrophobic interactions: E:Y.90, B:I.45 Hydrogen bonds: E:H.62, E:H.62, B:L.43, B:I.45 Salt bridges: E:E.63 Water bridges: B:L.43 GD1.7: 12 residues within 4Å: Chain F: C.21, D.28, L.61, H.62, E.63, Y.90 Chain I: L.2, V.42, L.43, A.44, I.45, E.46 8 PLIP interactions: 4 interactions with chain F, 4 interactions with chain I Hydrophobic interactions: F:L.61, I:I.45 Hydrogen bonds: F:H.62, F:H.62, I:L.43, I:I.45 Salt bridges: F:E.63 Water bridges: I:L.43 GD1.8: 12 residues within 4Å: Chain A: V.42, L.43, A.44, I.45, E.46 Chain G: C.21, I.23, D.28, L.61, H.62, E.63, Y.90 10 PLIP interactions: 6 interactions with chain G, 4 interactions with chain A Hydrophobic interactions: G:L.61, G:Y.90, A:I.45 Hydrogen bonds: G:H.62, G:H.62, A:L.43, A:I.45 Water bridges: G:D.28, A:L.43 Salt bridges: G:E.63 GD1.9: 13 residues within 4Å: Chain E: L.2, V.42, L.43, A.44, I.45, E.46 Chain H: C.21, P.22, D.28, L.61, H.62, E.63, Y.90 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain H Hydrophobic interactions: E:I.45 Hydrogen bonds: E:L.43, E:I.45, H:H.62 Salt bridges: H:E.63 GD1.10: 13 residues within 4Å: Chain H: 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 9 PLIP interactions: 5 interactions with chain I, 4 interactions with chain H Hydrophobic interactions: I:I.23, I:L.61, H:I.45 Hydrogen bonds: I:H.62, I:H.62, H:L.43, H:I.45 Salt bridges: I:E.63 Water bridges: H:L.43 GD1.12: 12 residues within 4Å: Chain G: L.2, V.42, L.43, A.44, I.45, E.46 Chain J: C.21, D.28, L.61, H.62, E.63, Y.90 9 PLIP interactions: 4 interactions with chain G, 5 interactions with chain J Hydrophobic interactions: G:I.45, J:L.61 Hydrogen bonds: G:L.43, G:I.45, J:H.62, J:H.62 Water bridges: G:L.43, J:D.28 Salt bridges: J:E.63

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

NA.4: 5 residues within 4Å: Chain C: E.31, V.32, S.33, T.85, K.87 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.31, C:E.31 NA.11: 5 residues within 4Å: Chain I: E.31, V.32, S.33, T.85, K.87 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:S.33, I:T.85

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
B

B
D

C
E

D
F

E
G

F
H

G
I

H
K

I
L

J
O

Archeaosine synthase QueF-Like

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