SMTL ID : 6ybs.1

Structure of a human 48S translational initiation complex - head

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

MG.1: 3 residues within 4Å: Chain N: T.136, T.139 Chain R: A.1522 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:T.136, N:T.139 MG.3: 2 residues within 4Å: Chain R: A.1217, U.1643 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain R: C.1219, G.1221 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain R: G.1224, U.1225 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain R: G.1226, G.1227 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain R: C.1216, A.1250, U.1340 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain R: A.1253, C.1254 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain R: A.1258 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain R: A.1259, A.1260 No protein-ligand interaction detected (PLIP) MG.11: 5 residues within 4Å: Chain R: C.1261, C.1262, U.1263, C.1264, G.1517 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain R: C.1262 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain R: A.1260, G.1516 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain R: U.1326, U.1494 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain R: G.1330, C.1331, G.1490, G.1491 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain R: C.1331, A.1489, G.1490, G.1491 No protein-ligand interaction detected (PLIP) MG.17: 4 residues within 4Å: Chain R: G.1335, C.1336, G.1491, U.1492 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain R: G.1351, G.1352 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain R: G.1387, C.1389, C.1482 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain R: G.1385, G.1387 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain R: G.1233, C.1518, U.1519 No protein-ligand interaction detected (PLIP) MG.22: 4 residues within 4Å: Chain L: I.78, G.80 Chain R: A.1588, A.1589 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:G.80 MG.23: 3 residues within 4Å: Chain R: G.1603, G.1605, G.1606 No protein-ligand interaction detected (PLIP) MG.24: 2 residues within 4Å: Chain R: G.1604, G.1605 No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Chain R: U.1653 No protein-ligand interaction detected (PLIP) MG.26: 2 residues within 4Å: Chain R: U.1659, A.1664 No protein-ligand interaction detected (PLIP) MG.27: 3 residues within 4Å: Chain R: G.1290, G.1302, C.1303 No protein-ligand interaction detected (PLIP) MG.28: 2 residues within 4Å: Chain R: C.1292, A.1293 No protein-ligand interaction detected (PLIP) MG.29: 4 residues within 4Å: Chain R: G.1330, G.1334, U.1492, U.1496 No protein-ligand interaction detected (PLIP) MG.30: 5 residues within 4Å: Chain O: A.162, N.165, K.167 Chain R: C.1534, U.1535 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:A.162, O:N.165, O:K.167

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain P: C.121, C.126, C.141, K.143, C.144 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.121, P:C.126, P:C.141, P:C.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brito Querido, J. et al., Structure of a human 48Stranslational initiation complex. Science (2020)

Release Date

2020-09-16

Peptides

Eukaryotic translation initiation factor 3 subunit D: A
Receptor of activated protein C kinase 1: B
40S ribosomal protein S28: C
40S ribosomal protein S17: D
40S ribosomal protein S20: E
Eukaryotic translation initiation factor 3 subunit G: F
40S ribosomal protein S10: G
40S ribosomal protein S12: H
40S ribosomal protein S29: I
40S ribosomal protein S15: J
40S ribosomal protein S3: K
40S ribosomal protein S19: L
40S ribosomal protein S25: M
40S ribosomal protein S18: N
40S ribosomal protein S5: O
Ubiquitin-40S ribosomal protein S27a: P
40S ribosomal protein S16: Q

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
x

B
c

C
n

D
X

E
h

F
o

G
a

H
m

I
i

J
b

K
Z

L
d

M
e

N
f

O
V

P
k

Q
Y

Eukaryotic translation initiation factor 3 subunit D

Receptor of activated protein C kinase 1

40S ribosomal protein S28

40S ribosomal protein S17

40S ribosomal protein S20

Eukaryotic translation initiation factor 3 subunit G

40S ribosomal protein S10

40S ribosomal protein S12

40S ribosomal protein S29

40S ribosomal protein S15

40S ribosomal protein S3

40S ribosomal protein S19

40S ribosomal protein S25

40S ribosomal protein S18

40S ribosomal protein S5

Ubiquitin-40S ribosomal protein S27a

40S ribosomal protein S16

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