SMTL ID : 5yni.1

Crystal structure of MERS-CoV nsp16/nsp10 complex bound to SAM and m7GpppG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

hetero-1-1-mer

Ligands

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.1: 18 residues within 4Å: Chain A: N.43, Y.47, G.71, A.72, G.73, P.80, G.81, N.98, D.99, L.100, N.101, G.113, D.114, C.115, D.130, M.131, Y.132 Ligands: GTG.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:N.43, A:Y.47, A:Y.47, A:G.71, A:G.73, A:G.81, A:L.100, A:N.101, A:D.114, A:D.114, A:C.115, A:D.130, A:Y.132 Salt bridges: A:D.130

1 x GTG: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE(Non-covalent)

GTG.2: 17 residues within 4Å: Chain A: C.25, E.26, L.27, Y.30, K.31, K.46, Y.132, K.137, V.139, K.170, T.172, E.173, H.174, S.201, S.202, E.203 Ligands: SAM.1 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:L.27, A:Y.30, A:K.31, A:K.46, A:K.170, A:T.172, A:H.174, A:S.175, A:S.201, A:S.202, A:E.203 Water bridges: A:N.43, A:K.76, A:K.76 Salt bridges: A:K.31, A:K.137, A:K.137, A:K.137 pi-Stacking: A:Y.30, A:Y.30

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain B: C.74, C.77, H.83, C.90 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.74, B:C.77, B:H.83, B:C.90 ZN.4: 4 residues within 4Å: Chain B: C.117, C.120, C.128, C.130 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.117, B:C.120, B:C.128, B:C.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wei, S.M. et al., Structural insights into the molecular mechanism of MERS Coronavirus RNA ribose 2'-O-methylation by nsp16/nsp10 protein complex. To Be Published

Release Date

2018-12-05

Peptides

nsp16 protein: A
nsp10 protein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

nsp16 protein

nsp10 protein

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