SMTL ID : 6zok.1

SARS-CoV-2-Nsp1-40S complex, focused on body

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

109 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.1: 1 residues within 4Å: Chain A: C.472 No protein-ligand interaction detected (PLIP) MG.2: 4 residues within 4Å: Chain A: U.667, A.668, A.669, A.670 No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain A: G.94, G.451 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain A: G.999 No protein-ligand interaction detected (PLIP) MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain A: A.449 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain A: G.434, A.435, C.450 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain A: G.94 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain A: G.1352 No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain A: A.508, G.509 Ligands: MG.90 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain A: G.673, A.1082 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain A: U.1830, A.1831, A.1832, G.1837 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain A: G.16 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain A: C.1841, C.1842, G.1857, G.1858 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain A: U.1101, G.1102, G.1130, G.1131 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain A: G.419, A.654, G.656 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain A: C.48, A.473 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain A: G.1166, G.1167 No protein-ligand interaction detected (PLIP) MG.20: 4 residues within 4Å: Chain A: A.99, U.100, U.101, C.409 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain A: G.410, A.426, U.427 No protein-ligand interaction detected (PLIP) MG.22: 1 residues within 4Å: Chain A: G.1048 No protein-ligand interaction detected (PLIP) MG.23: 4 residues within 4Å: Chain A: C.492, U.495, C.496, G.506 No protein-ligand interaction detected (PLIP) MG.24: 3 residues within 4Å: Chain A: G.601, A.604, A.605 No protein-ligand interaction detected (PLIP) MG.25: 3 residues within 4Å: Chain A: A.27, A.484, A.485 No protein-ligand interaction detected (PLIP) MG.26: 1 residues within 4Å: Chain A: G.20 No protein-ligand interaction detected (PLIP) MG.27: 3 residues within 4Å: Chain A: C.663, U.1156, G.1157 No protein-ligand interaction detected (PLIP) MG.28: 1 residues within 4Å: Chain A: A.1035 No protein-ligand interaction detected (PLIP) MG.29: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.30: 3 residues within 4Å: Chain A: G.684, A.685, A.864 No protein-ligand interaction detected (PLIP) MG.31: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.32: 1 residues within 4Å: Chain A: U.1839 No protein-ligand interaction detected (PLIP) MG.33: 3 residues within 4Å: Chain A: U.57, U.87, G.88 No protein-ligand interaction detected (PLIP) MG.34: 1 residues within 4Å: Chain A: A.653 No protein-ligand interaction detected (PLIP) MG.35: 1 residues within 4Å: Chain A: G.504 No protein-ligand interaction detected (PLIP) MG.36: 6 residues within 4Å: Chain A: A.1832, G.1836, G.1837, U.1839, U.1840 Ligands: MG.52 No protein-ligand interaction detected (PLIP) MG.37: 5 residues within 4Å: Chain A: G.90, G.444, A.445, G.446 Ligands: MG.47 No protein-ligand interaction detected (PLIP) MG.38: 1 residues within 4Å: Chain A: A.672 No protein-ligand interaction detected (PLIP) MG.39: 4 residues within 4Å: Chain A: U.1864, A.1866 Chain R: G.8, K.33 No protein-ligand interaction detected (PLIP) MG.40: 1 residues within 4Å: Chain A: G.1104 No protein-ligand interaction detected (PLIP) MG.41: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.42: 3 residues within 4Å: Chain A: G.1693, U.1694, G.1862 No protein-ligand interaction detected (PLIP) MG.43: 3 residues within 4Å: Chain A: A.1024, U.1025 Chain K: M.4 No protein-ligand interaction detected (PLIP) MG.44: 4 residues within 4Å: Chain A: G.1736, G.1737, G.1796, U.1797 No protein-ligand interaction detected (PLIP) MG.45: 3 residues within 4Å: Chain A: G.985, G.986, A.987 No protein-ligand interaction detected (PLIP) MG.46: 4 residues within 4Å: Chain A: G.1693, A.1834, A.1835, A.1863 No protein-ligand interaction detected (PLIP) MG.47: 5 residues within 4Å: Chain A: G.90, A.91, A.92, G.446 Ligands: MG.37 No protein-ligand interaction detected (PLIP) MG.48: 2 residues within 4Å: Chain A: A.1036, U.1072 No protein-ligand interaction detected (PLIP) MG.49: 3 residues within 4Å: Chain A: C.1833, U.1839, U.1840 No protein-ligand interaction detected (PLIP) MG.50: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.51: 1 residues within 4Å: Chain A: A.668 No protein-ligand interaction detected (PLIP) MG.52: 5 residues within 4Å: Chain A: A.1831, A.1832, U.1840, C.1853 Ligands: MG.36 No protein-ligand interaction detected (PLIP) MG.53: 2 residues within 4Å: Chain A: A.1028, G.1029 No protein-ligand interaction detected (PLIP) MG.54: 2 residues within 4Å: Chain A: A.812, A.813 No protein-ligand interaction detected (PLIP) MG.55: 3 residues within 4Å: Chain A: G.41, G.482, A.485 No protein-ligand interaction detected (PLIP) MG.56: 3 residues within 4Å: Chain A: C.472, A.476, G.477 No protein-ligand interaction detected (PLIP) MG.57: 2 residues within 4Å: Chain A: A.679, G.680 No protein-ligand interaction detected (PLIP) MG.58: 3 residues within 4Å: Chain A: U.612, G.613, A.629 No protein-ligand interaction detected (PLIP) MG.59: 3 residues within 4Å: Chain A: C.497 Chain E: R.30, T.81 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:R.30 MG.60: 1 residues within 4Å: Chain A: G.1354 No protein-ligand interaction detected (PLIP) MG.61: 2 residues within 4Å: Chain A: G.7, G.16 No protein-ligand interaction detected (PLIP) MG.62: 3 residues within 4Å: Chain A: A.523, C.593, A.594 No protein-ligand interaction detected (PLIP) MG.63: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.64: 4 residues within 4Å: Chain A: G.601, G.602, C.603, A.605 No protein-ligand interaction detected (PLIP) MG.65: 1 residues within 4Å: Chain A: A.149 No protein-ligand interaction detected (PLIP) MG.66: 1 residues within 4Å: Chain A: A.99 No protein-ligand interaction detected (PLIP) MG.67: 4 residues within 4Å: Chain A: G.993, C.994, G.1102, C.1103 No protein-ligand interaction detected (PLIP) MG.68: 2 residues within 4Å: Chain A: G.935, G.936 No protein-ligand interaction detected (PLIP) MG.69: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.70: 3 residues within 4Å: Chain A: U.9, G.10, A.11 No protein-ligand interaction detected (PLIP) MG.71: 4 residues within 4Å: Chain A: A.672, G.673, C.674, C.1085 No protein-ligand interaction detected (PLIP) MG.72: 2 residues within 4Å: Chain A: U.375, G.385 No protein-ligand interaction detected (PLIP) MG.73: 3 residues within 4Å: Chain A: G.656, G.662, U.1156 No protein-ligand interaction detected (PLIP) MG.74: 1 residues within 4Å: Chain A: A.564 No protein-ligand interaction detected (PLIP) MG.75: 2 residues within 4Å: Chain A: A.297, G.298 No protein-ligand interaction detected (PLIP) MG.76: 2 residues within 4Å: Chain A: A.173, C.174 No protein-ligand interaction detected (PLIP) MG.77: 1 residues within 4Å: Chain A: G.410 No protein-ligand interaction detected (PLIP) MG.78: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.79: 3 residues within 4Å: Chain A: C.417, G.419, G.420 No protein-ligand interaction detected (PLIP) MG.80: 5 residues within 4Å: Chain A: C.417, G.419, G.420, A.653, A.654 No protein-ligand interaction detected (PLIP) MG.81: 2 residues within 4Å: Chain A: C.622, G.623 No protein-ligand interaction detected (PLIP) MG.82: 1 residues within 4Å: Chain A: A.519 No protein-ligand interaction detected (PLIP) MG.83: 2 residues within 4Å: Chain A: G.597, G.598 No protein-ligand interaction detected (PLIP) MG.84: 1 residues within 4Å: Chain A: A.811 No protein-ligand interaction detected (PLIP) MG.85: 4 residues within 4Å: Chain A: U.1013, G.1014, U.1015 Chain K: S.12 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:S.12 MG.86: 5 residues within 4Å: Chain A: G.1166, G.1167, G.1168, U.1192 Chain P: K.25 No protein-ligand interaction detected (PLIP) MG.87: 3 residues within 4Å: Chain A: G.437, G.438, C.450 No protein-ligand interaction detected (PLIP) MG.88: 3 residues within 4Å: Chain A: U.100, A.433 Chain H: Y.21 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:Y.21 MG.89: 4 residues within 4Å: Chain A: C.1085, G.1086, A.1859, A.1860 No protein-ligand interaction detected (PLIP) MG.90: 5 residues within 4Å: Chain A: G.95, C.475, A.508, G.509 Ligands: MG.11 No protein-ligand interaction detected (PLIP) MG.91: 4 residues within 4Å: Chain A: U.51, G.52, C.53, C.472 No protein-ligand interaction detected (PLIP) MG.92: 3 residues within 4Å: Chain A: G.507, G.509, G.510 No protein-ligand interaction detected (PLIP) MG.93: 4 residues within 4Å: Chain A: U.43, A.45, A.46 Ligands: MG.99 No protein-ligand interaction detected (PLIP) MG.94: 3 residues within 4Å: Chain A: A.107, G.108, U.109 No protein-ligand interaction detected (PLIP) MG.95: 3 residues within 4Å: Chain A: U.1202, G.1203, U.1694 No protein-ligand interaction detected (PLIP) MG.96: 3 residues within 4Å: Chain A: G.114, U.115, C.382 No protein-ligand interaction detected (PLIP) MG.97: 3 residues within 4Å: Chain A: G.411, G.412, G.425 No protein-ligand interaction detected (PLIP) MG.98: 5 residues within 4Å: Chain A: A.54, G.94, G.474, G.507, A.508 No protein-ligand interaction detected (PLIP) MG.99: 5 residues within 4Å: Chain A: A.42, U.43, A.46, C.98 Ligands: MG.93 No protein-ligand interaction detected (PLIP) MG.100: 3 residues within 4Å: Chain A: G.41, A.42, U.97 No protein-ligand interaction detected (PLIP) MG.101: 4 residues within 4Å: Chain A: A.1050, A.1062, C.1853, U.1854 No protein-ligand interaction detected (PLIP) MG.102: 4 residues within 4Å: Chain A: A.435, G.436, A.473, G.474 No protein-ligand interaction detected (PLIP) MG.103: 5 residues within 4Å: Chain A: C.118, U.119, U.120, A.343, U.344 No protein-ligand interaction detected (PLIP) MG.104: 2 residues within 4Å: Chain A: C.315 Chain F: Q.177 No protein-ligand interaction detected (PLIP) MG.105: 5 residues within 4Å: Chain A: G.959, U.960 Chain L: N.38, D.65, E.68 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:N.38, L:D.65 MG.106: 3 residues within 4Å: Chain A: G.958, G.959 Chain L: E.68 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:E.68, L:E.68 MG.107: 5 residues within 4Å: Chain A: G.420, C.660 Chain J: R.97, K.98, N.100 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:K.98 MG.108: 4 residues within 4Å: Chain A: C.614, G.625 Chain P: P.62, N.63 No protein-ligand interaction detected (PLIP) MG.109: 3 residues within 4Å: Chain A: C.18, U.657 Chain P: Q.26 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.110: 4 residues within 4Å: Chain R: C.22, C.25, C.73, C.76 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.22, R:C.25, R:C.73, R:C.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schubert, K. et al., SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-07-29

Peptides

40S ribosomal protein SA: B
40S ribosomal protein S3a: C
40S ribosomal protein S2: D
40S ribosomal protein S4, X isoform: E
40S ribosomal protein S6: F
40S ribosomal protein S7: G
40S ribosomal protein S8: H
40S ribosomal protein S9: I
40S ribosomal protein S11: J
40S ribosomal protein S13: K
40S ribosomal protein S14: L
40S ribosomal protein S17: M
40S ribosomal protein S21: N
40S ribosomal protein S15a: O
40S ribosomal protein S23: P
40S ribosomal protein S24: Q
40S ribosomal protein S26: R
40S ribosomal protein S27: S
40S ribosomal protein S30: T
Non-structural protein 1: U
60S ribosomal protein L41: V

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

C
B

D
C

E
E

F
G

G
H

H
I

I
J

J
L

K
N

L
O

M
R

N
V

O
W

P
X

Q
Y

R
a

S
b

T
e

U
j

V
h

40S ribosomal protein SA

40S ribosomal protein S3a

40S ribosomal protein S2

40S ribosomal protein S4, X isoform

40S ribosomal protein S6

40S ribosomal protein S7

40S ribosomal protein S8

40S ribosomal protein S9

40S ribosomal protein S11

40S ribosomal protein S13

40S ribosomal protein S14

40S ribosomal protein S17

40S ribosomal protein S21

40S ribosomal protein S15a

40S ribosomal protein S23

40S ribosomal protein S24

40S ribosomal protein S26

40S ribosomal protein S27

40S ribosomal protein S30

Non-structural protein 1

60S ribosomal protein L41

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