SMTL ID : 7xxk.1 (2 other biounits)

Crystal structure of SARS-CoV-2 N-CTD in complex with GMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

1 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.1: 5 residues within 4Å: Chain A: K.12, K.13, R.18, T.19, Y.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.13 Water bridges: A:K.12

2 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.2: 5 residues within 4Å: Chain A: R.15, T.38, W.86 Chain B: M.73, K.94 15 PLIP interactions: 10 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:R.15, A:T.38, B:K.94, B:K.94 Water bridges: A:R.15, A:R.15, A:R.15, A:T.38, A:T.38, B:A.92, B:L.95 pi-Stacking: A:W.86 pi-Cation interactions: A:R.15, A:R.15 Salt bridges: B:K.94 5GP.3: 6 residues within 4Å: Chain A: M.73, I.93, K.94 Chain B: R.15, T.38, W.86 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.15, B:R.15, B:T.38, A:K.94, A:K.94 Water bridges: B:R.15, A:A.92 pi-Stacking: B:W.86 pi-Cation interactions: B:R.15 Salt bridges: A:K.94

5 x K: POTASSIUM ION(Non-covalent)

K.4: 4 residues within 4Å: Chain A: S.66, A.67, S.68 Chain B: T.19 No protein-ligand interaction detected (PLIP) K.5: 3 residues within 4Å: Chain A: Q.59, D.104, Q.105 No protein-ligand interaction detected (PLIP) K.6: 3 residues within 4Å: Chain A: T.27, R.32, R.33 No protein-ligand interaction detected (PLIP) K.7: 2 residues within 4Å: Chain A: E.79, V.80 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.79 K.8: 4 residues within 4Å: Chain A: T.19 Chain B: S.66, A.67, S.68 No protein-ligand interaction detected (PLIP)

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

CL.9: 3 residues within 4Å: Chain B: K.55, H.56, Q.59 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain B: K.111 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: R.18, T.19, Y.24 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, R.J. et al., Crystal structure of SARS-CoV-2 N-CTD in complex with GMP. To Be Published

Release Date

2022-06-29

Peptides

Nucleoprotein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nucleoprotein

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