SMTL ID : 5t2t.1 (1 other biounit)

Crystal structure of Lymphocytic choriomeningitis mammarenavirus endonuclease bound to compound L742001

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: D.96, E.109, C.110 Ligands: MN.2, 0N8.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.96, A:D.96, A:C.110, H2O.2, H2O.2 MN.2: 4 residues within 4Å: Chain A: I.94, D.96 Ligands: MN.1, 0N8.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.96, H2O.1, H2O.1, H2O.3

1 x 0N8: (2Z)-4-[1-benzyl-4-(4-chlorobenzyl)piperidin-4-yl]-2-hydroxy-4-oxobut-2-enoic acid(Non-covalent)

0N8.3: 14 residues within 4Å: Chain A: K.51, S.54, R.55, E.58, L.92, I.94, D.96, C.110, K.122 Chain B: E.189, Y.190 Ligands: MN.1, MN.2, GOL.4 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.92, A:I.94, B:Y.190 Hydrogen bonds: A:D.96 Water bridges: A:E.58, A:C.110, A:K.122, A:K.122, A:K.129 Salt bridges: A:K.122 Halogen bonds: A:K.51

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: R.113, K.122, E.125 Chain B: E.187, S.188, E.189, R.192 Ligands: 0N8.3 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:E.189, B:E.189, A:K.122, A:E.125 Water bridges: B:R.192, A:R.113, A:D.126 GOL.5: 3 residues within 4Å: Chain B: R.16, L.20, L.37 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.37

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain B: G.66, K.99 Ligands: NA.8 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: E.161, F.165 Ligands: NA.9 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.8: 1 residues within 4Å: Ligands: CL.6 2 PLIP interactions: 2 interactions with chain B Water bridges: B:A.62, B:C.67 NA.9: 2 residues within 4Å: Chain B: E.161 Ligands: CL.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saez-Ayala, M. et al., Crystal structures ofLymphocytic choriomeningitis virusendonuclease domain complexed with diketo-acid ligands. IUCrJ (2018)

Release Date

2017-09-13

Peptides

RNA-directed RNA polymerase L: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

RNA-directed RNA polymerase L

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