SMTL ID : 6bec.1

Crystal structure of VACV D13 in complex with Rifabutin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.91 Å

Oligo State

homo-trimer

Ligands

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

FMT.1: 5 residues within 4Å: Chain A: P.113, Y.298, Y.308, D.450, F.458 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.308 Water bridges: A:K.118, A:K.118 FMT.5: 7 residues within 4Å: Chain B: S.334, N.371, M.374, Y.432, N.433, G.434, N.436 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.334, B:N.433, B:G.434, B:N.436, B:N.436 FMT.6: 5 residues within 4Å: Chain B: R.258, V.260, T.270, V.271, T.272 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.258, B:T.270, B:T.272 FMT.9: 4 residues within 4Å: Chain C: I.383, Y.384, N.385, K.388 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.385 FMT.10: 5 residues within 4Å: Chain C: P.113, Y.298, Y.308, D.450, F.458 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.298, C:Y.308 Water bridges: C:K.118 FMT.11: 3 residues within 4Å: Chain C: T.503, N.505, F.506 1 PLIP interactions: 1 interactions with chain C Water bridges: C:F.506

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

EDO.2: 6 residues within 4Å: Chain A: Y.384, N.414, I.416, I.420, H.541, I.543 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.384, A:N.414, A:H.541, A:I.543 EDO.3: 7 residues within 4Å: Chain A: K.388, K.389, F.390, S.391, S.410, H.411, S.412 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.389, A:S.391 EDO.4: 7 residues within 4Å: Chain A: P.59, Q.60, Y.61 Chain B: Y.478, L.502, T.503, F.504 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.61, B:T.503 EDO.7: 8 residues within 4Å: Chain B: Y.384, N.414, I.416, D.417, I.420, H.541, P.542, I.543 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.414, B:H.541, B:I.543 EDO.12: 9 residues within 4Å: Chain C: Y.384, K.389, N.414, I.416, D.417, I.420, H.541, P.542, I.543 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.389, C:K.389, C:N.414, C:H.541, C:I.543 EDO.13: 8 residues within 4Å: Chain C: E.336, I.348, Q.349, T.370, M.374, I.383, N.385, K.388 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.336, C:Q.349, C:N.385 EDO.14: 7 residues within 4Å: Chain A: Y.478, L.502, T.503, F.504 Chain C: P.59, Q.60, Y.61 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Y.61, C:Y.61, A:T.503

1 x RBT: RIFABUTIN(Non-covalent)

RBT.8: 14 residues within 4Å: Chain A: V.49, E.190, F.193, P.508, F.511, F.512 Chain B: V.49, F.193, F.511 Chain C: Q.52, F.193, P.508, I.510, F.511 13 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: B:V.49, B:F.193, B:F.511, A:V.49, A:F.193, A:P.508, A:F.511, A:F.511, A:F.512, C:F.193, C:I.510, C:F.511, C:F.511

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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