SMTL ID : 6bee.1

Crystal structure of VACV D13 in complex with Rifaximin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.11 Å

Oligo State

homo-trimer

Ligands

5 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 5 residues within 4Å: Chain A: P.90, Y.275, Y.285, D.427, F.435 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.275, A:Y.285 FMT.5: 6 residues within 4Å: Chain B: S.311, M.351, Y.409, N.410, G.411, N.413 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.311, B:N.410, B:G.411, B:N.413 FMT.7: 5 residues within 4Å: Chain C: I.360, Y.361, N.362, K.365, K.366 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.362 FMT.8: 4 residues within 4Å: Chain C: Y.275, Y.285, I.425, D.427 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.275, C:Y.285, C:Y.285 Water bridges: C:K.95 FMT.9: 3 residues within 4Å: Chain A: K.471 Chain C: N.123, N.124 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.123

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

EDO.2: 8 residues within 4Å: Chain A: Y.361, N.391, I.393, D.394, I.397, H.518, P.519, I.520 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.361, A:N.391, A:H.518, A:I.520 EDO.3: 1 residues within 4Å: Ligands: RXM.4 No protein-ligand interaction detected (PLIP) EDO.6: 8 residues within 4Å: Chain B: Y.361, N.391, I.393, D.394, I.397, H.518, P.519, I.520 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.391, B:N.391, B:H.518, B:I.520 EDO.10: 8 residues within 4Å: Chain C: Y.361, N.391, I.393, D.394, I.397, H.518, P.519, I.520 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.391, C:H.518, C:I.520

1 x RXM: (2S,16Z,18E,20S,21S,22R,23R,24R,25S,26R,27S,28E)-5,6,21,23-tetrahydroxy-27-methoxy-2,4,11,16,20,22,24,26-octamethyl-1,1 5-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)furo[2'',3'':7',8']naphtho[1',2':4,5]imidazo[1,2-a]pyridin-2 5-yl acetate(Non-covalent)

RXM.4: 12 residues within 4Å: Chain A: Q.29, E.167, F.170, F.488, F.489 Chain B: V.26, F.488 Chain C: V.26, Q.29, F.170, F.488 Ligands: EDO.3 12 PLIP interactions: 6 interactions with chain A, 3 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: A:F.170, A:F.488, A:F.488, A:F.488, A:F.488, C:V.26, C:F.170, C:F.488, B:V.26, B:F.488, B:F.488 Hydrogen bonds: A:Q.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garriga, D. et al., Structural basis for the inhibition of poxvirus assembly by the antibiotic rifampicin. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-07-18

Peptides

Scaffold protein D13: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Scaffold protein D13

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