SMTL ID : 6bei.1

Crystal structure of VACV D13 in its apo (unbound) form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

homo-trimer

Ligands

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

FMT.1: 6 residues within 4Å: Chain A: P.90, Y.275, Q.280, Y.285, D.427, F.435 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.275, A:Y.285 Water bridges: A:K.95 FMT.2: 6 residues within 4Å: Chain A: K.262, P.263, D.427, P.428, F.429, I.430 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.262, A:I.430 FMT.3: 5 residues within 4Å: Chain A: H.70, N.124, Y.159 Chain B: L.468, K.471 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.70, A:N.124, B:K.471 FMT.4: 2 residues within 4Å: Chain A: V.166, E.167 No protein-ligand interaction detected (PLIP) FMT.5: 6 residues within 4Å: Chain A: Y.455, L.479, T.480 Chain C: P.36, Q.37, Y.38 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:T.480, A:T.480, C:Y.38 FMT.7: 6 residues within 4Å: Chain B: K.262, P.263, D.427, P.428, F.429, I.430 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.262, B:P.263, B:I.430 Water bridges: B:Y.265 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: 5 residues within 4Å: Chain C: Y.275, Y.285, I.425, D.427, F.435 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.11: 6 residues within 4Å: Chain C: W.110, I.112, N.120, K.161, T.162, P.163 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.120, C:K.161

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

EDO.6: 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.8: 7 residues within 4Å: Chain B: Y.361, N.391, I.393, D.394, I.397, H.518, 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.12: 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 EDO.13: 3 residues within 4Å: Chain B: D.168 Chain C: F.483, P.485 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.168

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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