SMTL ID : 6zol.1

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

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-mer

Ligands

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

MG.1: 4 residues within 4Å: Chain A: C.1261, C.1262, U.1263, G.1517 No protein-ligand interaction detected (PLIP) MG.2: 2 residues within 4Å: Chain A: G.1387, A.1388 No protein-ligand interaction detected (PLIP) MG.3: 5 residues within 4Å: Chain A: G.1330, G.1335, C.1336, G.1491, U.1492 No protein-ligand interaction detected (PLIP) MG.4: 6 residues within 4Å: Chain A: G.1603, G.1604, G.1605, G.1606 Chain I: R.38 Ligands: MG.30 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain A: U.1539, G.1540 No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain A: C.1655, G.1656, U.1667, U.1668, G.1669 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain A: U.1519 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain A: G.1226, G.1227 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain A: C.1262, G.1515 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain A: A.1259, A.1260 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Chain A: A.1258 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain A: A.1537, G.1604, G.1605 Chain J: E.44 Ligands: MG.42 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain A: A.1651, G.1652, U.1653 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain A: G.1510, U.1511 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain A: C.1337, G.1338, G.1490 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain A: C.1331, A.1489, G.1490, G.1491 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain A: G.1385, G.1387 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain A: G.1330, G.1334, G.1335, U.1496 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Chain A: C.1219 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain A: C.1216, A.1217, U.1643 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain A: U.1442, C.1443 No protein-ligand interaction detected (PLIP) MG.22: 5 residues within 4Å: Chain A: U.1530, A.1531, G.1606 Chain J: R.84, G.86 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:G.86 MG.23: 2 residues within 4Å: Chain A: A.1253, C.1254 No protein-ligand interaction detected (PLIP) MG.24: 2 residues within 4Å: Chain A: G.1224, U.1225 No protein-ligand interaction detected (PLIP) MG.25: 3 residues within 4Å: Chain A: G.1330, C.1331, G.1490 No protein-ligand interaction detected (PLIP) MG.26: 3 residues within 4Å: Chain A: U.1659, A.1663, A.1664 No protein-ligand interaction detected (PLIP) MG.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.28: 3 residues within 4Å: Chain A: U.1326, U.1494, U.1496 No protein-ligand interaction detected (PLIP) MG.29: 2 residues within 4Å: Chain A: U.1360, G.1361 No protein-ligand interaction detected (PLIP) MG.30: 4 residues within 4Å: Chain A: U.1602, G.1603, G.1605 Ligands: MG.4 No protein-ligand interaction detected (PLIP) MG.31: 3 residues within 4Å: Chain A: C.1493, U.1494, U.1499 No protein-ligand interaction detected (PLIP) MG.32: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.33: 3 residues within 4Å: Chain A: C.1538, U.1539 Chain J: Y.48 No protein-ligand interaction detected (PLIP) MG.34: 2 residues within 4Å: Chain A: U.1339, U.1340 No protein-ligand interaction detected (PLIP) MG.35: 4 residues within 4Å: Chain A: U.1225, G.1226, G.1227, G.1638 No protein-ligand interaction detected (PLIP) MG.36: 1 residues within 4Å: Chain A: U.1672 No protein-ligand interaction detected (PLIP) MG.37: 3 residues within 4Å: Chain A: G.1255, G.1257, U.1494 No protein-ligand interaction detected (PLIP) MG.38: 1 residues within 4Å: Chain A: A.1260 No protein-ligand interaction detected (PLIP) MG.39: 2 residues within 4Å: Chain A: C.1273, C.1316 No protein-ligand interaction detected (PLIP) MG.40: 2 residues within 4Å: Chain A: G.1536, C.1591 No protein-ligand interaction detected (PLIP) MG.41: 5 residues within 4Å: Chain A: G.1328, U.1329, C.1493, G.1500, C.1501 No protein-ligand interaction detected (PLIP) MG.42: 3 residues within 4Å: Chain A: G.1604, G.1605 Ligands: MG.12 No protein-ligand interaction detected (PLIP) MG.43: 4 residues within 4Å: Chain A: C.1213, C.1682, U.1685, G.1686 No protein-ligand interaction detected (PLIP) MG.44: 4 residues within 4Å: Chain A: U.1519, A.1623 Chain I: G.133, H.135 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:G.133 MG.45: 5 residues within 4Å: Chain A: G.1269, G.1298, A.1299, C.1513, G.1514 No protein-ligand interaction detected (PLIP) MG.46: 5 residues within 4Å: Chain A: G.1233, C.1234, G.1245, C.1254, G.1255 No protein-ligand interaction detected (PLIP) MG.47: 4 residues within 4Å: Chain A: C.1234, A.1251, C.1252, C.1525 No protein-ligand interaction detected (PLIP) MG.48: 2 residues within 4Å: Chain A: U.1225, G.1528 No protein-ligand interaction detected (PLIP) MG.49: 4 residues within 4Å: Chain A: U.1367, U.1368, U.1371, U.1372 No protein-ligand interaction detected (PLIP) MG.50: 4 residues within 4Å: Chain A: G.1528, C.1529, C.1666, U.1667 No protein-ligand interaction detected (PLIP) MG.51: 5 residues within 4Å: Chain A: U.1243, U.1244, A.1265, U.1494 Chain O: K.1 No protein-ligand interaction detected (PLIP) MG.52: 3 residues within 4Å: Chain A: G.1517, C.1518, U.1622 No protein-ligand interaction detected (PLIP) MG.53: 3 residues within 4Å: Chain A: C.1261, G.1514, G.1515 No protein-ligand interaction detected (PLIP) MG.54: 5 residues within 4Å: Chain A: C.1534, U.1535 Chain C: A.162, N.165, K.167 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:A.162, C:N.165, C:K.167 MG.55: 4 residues within 4Å: Chain A: C.1521 Chain I: T.136, T.139, G.140 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:T.136, I:T.139 MG.56: 5 residues within 4Å: Chain A: U.1631, G.1632 Chain I: T.31, I.33, V.36 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:T.31, I:I.33, I:V.36 MG.57: 3 residues within 4Å: Chain A: A.1589 Chain J: I.78, G.80 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:G.80

2 x ZN: ZINC ION(Non-covalent)

ZN.58: 4 residues within 4Å: Chain N: C.20, C.23, C.38, C.41 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.20, N:C.23, N:C.38, N:C.41 ZN.59: 5 residues within 4Å: Chain O: C.44, S.46, C.49, C.64, C.67 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.44, O:C.49, O:C.64, O:C.67

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

2020-07-22

Peptides

40S ribosomal protein S3: B
40S ribosomal protein S5: C
40S ribosomal protein S10: D
40S ribosomal protein S12: E
40S ribosomal protein S15: F
40S ribosomal protein S16: G
40S ribosomal protein S17: H
40S ribosomal protein S18: I
40S ribosomal protein S19: J
40S ribosomal protein S20: K
40S ribosomal protein S25: L
40S ribosomal protein S28: M
40S ribosomal protein S29: N
Ribosomal protein S27a: O
Receptor of activated protein C kinase 1: P

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
D

C
F

D
K

E
M

F
P

G
Q

H
R

I
S

J
T

K
U

L
Z

M
c

N
d

O
f

P
g

40S ribosomal protein S3

40S ribosomal protein S5

40S ribosomal protein S10

40S ribosomal protein S12

40S ribosomal protein S15

40S ribosomal protein S16

40S ribosomal protein S17

40S ribosomal protein S18

40S ribosomal protein S19

40S ribosomal protein S20

40S ribosomal protein S25

40S ribosomal protein S28

40S ribosomal protein S29

Ribosomal protein S27a

Receptor of activated protein C kinase 1

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