SMTL ID : 6yu8.1

RNA Methyltransferase of Sudan Ebola Virus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

hetero-1-1-mer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: I.165, H.167, R.168, W.170, F.171, E.202, A.203, T.206 Chain B: F.29 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.167, A:W.170, A:F.171, A:T.206, A:T.206 Water bridges: A:R.168, A:S.172, A:E.202, B:R.27 GOL.4: 1 residues within 4Å: Chain A: T.306 No protein-ligand interaction detected (PLIP) GOL.5: 1 residues within 4Å: Chain A: T.306 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.306 GOL.16: 4 residues within 4Å: Chain A: S.270 Chain B: G.55, I.56, R.57 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:S.270 Hydrogen bonds: B:R.57, B:R.57, B:R.57 GOL.17: 5 residues within 4Å: Chain B: K.65, G.66, R.67, F.68, T.69 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.66, B:T.69 Water bridges: B:Y.60 GOL.18: 8 residues within 4Å: Chain A: F.171, K.175, N.210 Chain B: T.28, F.29, W.53, N.74, D.77 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.28, B:W.53, B:N.74, A:N.210

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

PEG.2: 6 residues within 4Å: Chain A: N.194, D.196, S.227, D.228, L.229, D.230 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.228, A:L.229, A:D.230 Water bridges: A:N.194, A:D.196, A:S.227 PEG.3: 7 residues within 4Å: Chain A: T.271, L.272, T.274 Chain B: F.47, T.58, S.59, T.104 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.59, A:L.272, A:T.274 Water bridges: B:S.59, B:D.62 PEG.19: 6 residues within 4Å: Chain A: Y.238 Chain B: A.100, L.101, Y.107, E.108, D.110 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:Y.238, B:D.110

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

NA.6: 3 residues within 4Å: Chain A: C.233, W.234, N.237 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.233, A:N.237 NA.7: 4 residues within 4Å: Chain A: E.122, P.136, R.137 Ligands: CL.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.122, A:R.137 Water bridges: A:E.122 NA.8: 5 residues within 4Å: Chain A: N.117, L.119, T.163, D.164, I.165 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.117, A:T.163, A:I.165 NA.9: 2 residues within 4Å: Chain A: Y.247 Ligands: CL.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.27 NA.10: 6 residues within 4Å: Chain A: P.179, N.180, D.181, A.182, H.211, I.212 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.182, A:H.211 NA.11: 2 residues within 4Å: Chain A: S.90, D.181 No protein-ligand interaction detected (PLIP) NA.20: 4 residues within 4Å: Chain A: T.274 Chain B: R.103, T.104 Ligands: CL.25 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.104, A:T.274 NA.21: 2 residues within 4Å: Chain B: T.69, N.84 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.69, B:T.69, B:N.84 NA.22: 1 residues within 4Å: Chain B: R.103 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.103 Water bridges: B:R.103 NA.23: 3 residues within 4Å: Chain B: S.17, L.18, Q.82 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.82 Water bridges: B:Q.82 NA.24: 4 residues within 4Å: Chain B: G.66, R.67, N.84, S.85 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.85, B:S.85

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

CL.12: 3 residues within 4Å: Chain A: A.120, E.122 Ligands: NA.7 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain A: F.27, S.245, G.246 Ligands: NA.9 Ligand excluded by PLIP CL.25: 4 residues within 4Å: Chain B: R.103, T.104, A.105 Ligands: NA.20 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.14: 4 residues within 4Å: Chain A: H.75, E.96, G.101, D.188 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.96, A:D.188, H2O.3 MG.15: 4 residues within 4Å: Chain A: L.82, W.83, Y.85, Y.109 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:L.82, A:Y.85, H2O.1, H2O.6, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Valle, C. et al., First insights into the structural features of Ebola virus methyltransferase activities. Nucleic Acids Res. (2021)

Release Date

2021-02-17

Peptides

Methyltransferase domain of the L protein: A
VHH antiboby: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Methyltransferase domain of the L protein

VHH antiboby