SMTL ID : 6beb.1

Crystal structure of VACV D13 in complex with Rifamycin SV

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-trimer

Ligands

1 x RFV: rifamycin SV(Non-covalent)

RFV.1: 14 residues within 4Å: Chain A: Q.52, E.190, F.193, P.508, F.511, F.512 Chain B: V.49, P.508, F.511 Chain C: F.193, F.511, F.512 Ligands: FMT.10, FMT.18 10 PLIP interactions: 2 interactions with chain C, 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: C:F.193, C:F.511, A:F.193, A:P.508, A:F.511, A:F.511, B:V.49, B:F.511, B:F.511 Hydrogen bonds: A:Q.52

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

FMT.2: 5 residues within 4Å: Chain A: P.113, Y.298, Y.308, D.450, F.458 Ligand excluded by PLIP FMT.3: 3 residues within 4Å: Chain A: T.536, Y.544, K.548 Ligand excluded by PLIP FMT.4: 6 residues within 4Å: Chain A: P.101, E.102, V.103, F.227, E.230, F.231 Ligand excluded by PLIP FMT.5: 5 residues within 4Å: Chain A: W.133, N.143, K.184, T.185, P.186 Ligand excluded by PLIP FMT.6: 4 residues within 4Å: Chain A: Q.60, Y.61 Chain B: L.502, T.503 Ligand excluded by PLIP FMT.7: 5 residues within 4Å: Chain A: L.502, T.503 Chain C: P.59, Q.60, Y.61 Ligand excluded by PLIP FMT.8: 6 residues within 4Å: Chain A: K.285, P.286, D.450, P.451, F.452, I.453 Ligand excluded by PLIP FMT.9: 3 residues within 4Å: Chain A: I.409, S.410, H.411 Ligand excluded by PLIP FMT.10: 1 residues within 4Å: Ligands: RFV.1 Ligand excluded by PLIP FMT.11: 7 residues within 4Å: Chain A: Y.384, I.416, I.420, M.537, H.541, P.542, I.543 Ligand excluded by PLIP FMT.12: 5 residues within 4Å: Chain A: H.93, N.147, Y.182 Chain B: L.491, K.494 Ligand excluded by PLIP FMT.13: 5 residues within 4Å: Chain A: I.383, Y.384, N.385, K.388, K.389 Ligand excluded by PLIP FMT.17: 2 residues within 4Å: Chain B: I.345, S.347 Ligand excluded by PLIP FMT.18: 2 residues within 4Å: Chain C: P.508 Ligands: RFV.1 Ligand excluded by PLIP FMT.19: 6 residues within 4Å: Chain B: Y.384, I.416, I.420, H.541, P.542, I.543 Ligand excluded by PLIP FMT.20: 5 residues within 4Å: Chain B: K.285, P.286, D.450, P.451, I.453 Ligand excluded by PLIP FMT.22: 4 residues within 4Å: Chain C: I.383, Y.384, N.385, K.388 Ligand excluded by PLIP FMT.23: 4 residues within 4Å: Chain C: P.113, Y.298, Y.308, D.450 Ligand excluded by PLIP FMT.24: 4 residues within 4Å: Chain A: K.494 Chain C: N.146, N.147, T.148 Ligand excluded by PLIP FMT.25: 4 residues within 4Å: Chain A: N.27 Chain B: Q.60 Chain C: Y.478, S.479 Ligand excluded by PLIP FMT.26: 6 residues within 4Å: Chain A: L.64, E.82, I.83, R.84, I.88 Chain C: Y.21 Ligand excluded by PLIP FMT.27: 6 residues within 4Å: Chain C: Y.384, I.416, I.420, H.541, P.542, I.543 Ligand excluded by PLIP FMT.28: 6 residues within 4Å: Chain C: S.334, M.374, Y.432, N.433, G.434, N.436 Ligand excluded by PLIP

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

EDO.14: 7 residues within 4Å: Chain A: R.513, P.514, T.515, T.516 Chain B: R.43 Chain C: P.54, L.56 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Water bridges: C:Y.57 Hydrogen bonds: A:R.513, A:T.516, A:T.516 EDO.15: 5 residues within 4Å: Chain A: T.426, S.427, N.430, Y.432, N.433 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.430 EDO.16: 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.388, A:S.391 EDO.21: 6 residues within 4Å: Chain B: P.59, Q.60, Y.61 Chain C: Y.478, L.502, T.503 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Y.61, C:T.503, C:T.503 EDO.29: 5 residues within 4Å: Chain C: I.348, Q.349, M.374, I.383, N.385 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.349, C:N.385 EDO.30: 5 residues within 4Å: Chain C: T.426, S.427, Q.428, N.430, Y.432 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.432

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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