SMTL ID : 5ltn.1

Crystal structure of Lymphocytic choriomeningitis mammarenavirus endonuclease complexed with DPBA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.96, E.109 Ligands: MG.2, XI7.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.96, A:E.109, H2O.1, H2O.1, H2O.2 MG.2: 4 residues within 4Å: Chain A: E.58, D.96 Ligands: MG.1, XI7.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.96, H2O.1, H2O.1, H2O.4 MG.11: 3 residues within 4Å: Chain B: E.58, D.96 Ligands: MG.12 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.58, B:D.96, H2O.5, H2O.8, H2O.9 MG.12: 3 residues within 4Å: Chain B: D.96, C.110 Ligands: MG.11 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.96, B:C.110, H2O.6, H2O.8, H2O.9

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: K.122, E.125 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.113, A:K.122, A:K.122, A:E.125 GOL.4: 8 residues within 4Å: Chain A: R.28, L.29, R.31, Q.32, K.51, R.55, H.69, H.71 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.28, A:R.31, A:Q.32, A:K.51, A:K.51, A:R.55 Water bridges: A:S.30 GOL.13: 1 residues within 4Å: Chain B: Y.154 No protein-ligand interaction detected (PLIP) GOL.14: 3 residues within 4Å: Chain B: E.161, W.162, F.165 No protein-ligand interaction detected (PLIP)

1 x XI7: 2-4-DIOXO-4-PHENYLBUTANOIC ACID(Non-covalent)

XI7.5: 7 residues within 4Å: Chain A: S.54, E.58, D.96, E.109, C.110 Ligands: MG.1, MG.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.58 Water bridges: A:K.122, A:K.122, A:K.122, A:K.122, A:K.122, A:K.129, A:K.129

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

CL.6: 2 residues within 4Å: Chain A: A.131, R.134 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain B: R.113, K.122 Ligand excluded by PLIP

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 4 residues within 4Å: Chain A: D.155, N.156, S.157, M.159 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.155 PEG.8: 6 residues within 4Å: Chain A: I.85, D.102, N.103, A.140, G.141 Ligands: NA.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.140

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

NA.9: 1 residues within 4Å: Ligands: PEG.8 No protein-ligand interaction detected (PLIP) NA.10: 2 residues within 4Å: Chain A: P.91, D.136 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saez-Ayala, M. et al., Crystal structures of Lymphocytic 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

Related Entries With Identical Sequence