SMTL ID : 6bef.1

Crystal structure of VACV D13 in complex with 3-formyl rifamycin SV

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.21 Å

Oligo State

homo-trimer

Ligands

1 x 3YI: (2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-8-formyl-5,6,9,17,19-pentahydroxy-23-methoxy-2,4,12,16,18,20,22-heptam ethyl-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)naphtho[2,1-b]furan-21-yl acetate(Non-covalent)

3YI.1: 10 residues within 4Å: Chain A: Q.29, E.167, P.485, F.488, F.489 Chain B: V.26, F.488 Chain C: F.170, F.488 Ligands: EDO.8 13 PLIP interactions: 3 interactions with chain B, 7 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: B:V.26, B:F.488, B:F.488, A:P.485, A:P.485, A:F.488, A:F.488, A:F.488, A:F.489, C:F.170, C:F.170, C:F.488 Hydrogen bonds: A:Q.29

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

FMT.2: 4 residues within 4Å: Chain A: 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.3: 6 residues within 4Å: Chain A: Y.455, L.479, T.480 Chain C: P.36, Q.37, Y.38 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:T.480, C:Y.38 FMT.6: 3 residues within 4Å: Chain B: N.123, N.124, T.125 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.125 FMT.9: 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.10: 3 residues within 4Å: Chain C: Y.275, Y.285, D.427 No protein-ligand interaction detected (PLIP) FMT.11: 3 residues within 4Å: Chain A: K.471 Chain C: N.123, N.124 No protein-ligand interaction detected (PLIP) FMT.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FMT.13: 3 residues within 4Å: Chain C: S.324, D.327, D.329 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.324, C:D.327

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

EDO.4: 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.5: 5 residues within 4Å: Chain A: T.403, S.404, N.407, Y.409, N.410 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.407 EDO.7: 8 residues within 4Å: Chain B: Y.361, N.391, I.393, D.394, I.397, H.518, P.519, I.520 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.391, B:H.518, B:I.520 EDO.8: 3 residues within 4Å: Chain B: E.167 Chain C: P.485 Ligands: 3YI.1 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.167 EDO.14: 8 residues within 4Å: Chain C: Y.361, N.391, I.393, I.397, M.514, 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 EDO.15: 2 residues within 4Å: Chain C: N.205, K.206 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.205, C:K.206 Water bridges: C:N.52

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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