SMTL ID : 9fco.1

Structure of E. coli 30S-IF1-IF3-mRNA-Kasugamycin complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x KSG: (1S,2R,3S,4R,5S,6S)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXYL 2-AMINO-4-{[CARBOXY(IMINO)METHYL]AMINO}-2,3,4,6-TETRADEOXY-ALPHA-D-ARABINO-HEXOPYRANOSIDE(Non-functional Binders)

KSG.1: 11 residues within 4Å: Chain A: A.769, A.771, G.898, U.1010, A.1011, G.1017, U.1018 Chain P: G.20, U.21, A.22, U.23 No protein-ligand interaction detected (PLIP)

53 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 3 residues within 4Å: Chain A: C.553, G.554, C.555 No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain A: C.307, C.329 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain A: A.524 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain A: G.339 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain A: G.708, G.1038, U.1039 No protein-ligand interaction detected (PLIP) MG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain A: G.301 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain A: G.427 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Chain A: A.745 No protein-ligand interaction detected (PLIP) MG.11: 5 residues within 4Å: Chain A: U.1010, A.1011, A.1012, G.1016, G.1017 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain A: A.549, A.550, A.551 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Chain A: A.791 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain A: G.830, G.841 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain A: G.534, A.536, A.537, U.539 No protein-ligand interaction detected (PLIP) MG.16: 1 residues within 4Å: Chain A: G.334 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain A: G.565, U.621, G.622 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain A: G.623 Ligands: K.55 No protein-ligand interaction detected (PLIP) MG.19: 4 residues within 4Å: Chain A: G.483, U.485, A.486, A.487 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain A: A.584, A.585, A.607 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain A: A.102, G.103, G.266 No protein-ligand interaction detected (PLIP) MG.22: 2 residues within 4Å: Chain A: A.95, G.308 No protein-ligand interaction detected (PLIP) MG.23: 1 residues within 4Å: Chain A: U.749 No protein-ligand interaction detected (PLIP) MG.24: 2 residues within 4Å: Chain A: G.242, C.244 No protein-ligand interaction detected (PLIP) MG.25: 2 residues within 4Å: Chain A: A.945, A.946 No protein-ligand interaction detected (PLIP) MG.26: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.27: 4 residues within 4Å: Chain A: A.572, A.573, G.574, U.575 No protein-ligand interaction detected (PLIP) MG.28: 3 residues within 4Å: Chain A: A.759, C.760, A.771 No protein-ligand interaction detected (PLIP) MG.29: 1 residues within 4Å: Chain A: G.21 No protein-ligand interaction detected (PLIP) MG.30: 2 residues within 4Å: Chain A: U.166, A.181 No protein-ligand interaction detected (PLIP) MG.31: 4 residues within 4Å: Chain A: C.58, A.59, C.363, U.364 No protein-ligand interaction detected (PLIP) MG.32: 2 residues within 4Å: Chain A: G.86, A.87 No protein-ligand interaction detected (PLIP) MG.33: 2 residues within 4Å: Chain A: A.160, C.161 No protein-ligand interaction detected (PLIP) MG.34: 4 residues within 4Å: Chain A: G.276, G.534, G.535, A.537 No protein-ligand interaction detected (PLIP) MG.35: 1 residues within 4Å: Chain A: A.549 No protein-ligand interaction detected (PLIP) MG.36: 1 residues within 4Å: Chain A: C.553 No protein-ligand interaction detected (PLIP) MG.37: 3 residues within 4Å: Chain A: C.557, U.734, C.735 No protein-ligand interaction detected (PLIP) MG.38: 3 residues within 4Å: Chain A: C.794, G.795, U.1040 No protein-ligand interaction detected (PLIP) MG.39: 2 residues within 4Å: Chain A: U.863, A.864 No protein-ligand interaction detected (PLIP) MG.40: 5 residues within 4Å: Chain A: A.1012, G.1017, A.1019, A.1020 Ligands: K.57 No protein-ligand interaction detected (PLIP) MG.41: 4 residues within 4Å: Chain A: U.493, G.494, A.509, A.510 No protein-ligand interaction detected (PLIP) MG.42: 1 residues within 4Å: Chain A: G.704 No protein-ligand interaction detected (PLIP) MG.43: 2 residues within 4Å: Chain A: A.391 Ligands: K.64 No protein-ligand interaction detected (PLIP) MG.44: 4 residues within 4Å: Chain A: G.130, G.131, G.163, A.183 No protein-ligand interaction detected (PLIP) MG.45: 2 residues within 4Å: Chain A: C.546, G.547 No protein-ligand interaction detected (PLIP) MG.46: 2 residues within 4Å: Chain A: U.13, U.14 No protein-ligand interaction detected (PLIP) MG.47: 2 residues within 4Å: Chain A: G.97, G.98 No protein-ligand interaction detected (PLIP) MG.48: 5 residues within 4Å: Chain A: C.47, C.48, U.49, U.100, G.101 No protein-ligand interaction detected (PLIP) MG.49: 2 residues within 4Å: Chain A: A.418, G.419 No protein-ligand interaction detected (PLIP) MG.50: 1 residues within 4Å: Chain A: G.236 No protein-ligand interaction detected (PLIP) MG.51: 3 residues within 4Å: Chain A: C.291, C.305, C.307 No protein-ligand interaction detected (PLIP) MG.52: 5 residues within 4Å: Chain A: C.1013, A.1014, G.1016, A.1019, A.1020 No protein-ligand interaction detected (PLIP) MG.53: 2 residues within 4Å: Chain A: A.757, G.777 No protein-ligand interaction detected (PLIP) MG.54: 3 residues within 4Å: Chain A: G.641, G.643, G.718 No protein-ligand interaction detected (PLIP)

25 x K: POTASSIUM ION(Non-functional Binders)(Non-covalent)

K.55: 5 residues within 4Å: Chain A: U.571, A.572, U.621, G.622 Ligands: MG.18 Ligand excluded by PLIP K.56: 4 residues within 4Å: Chain A: C.559, A.560, G.561, C.735 Ligand excluded by PLIP K.57: 5 residues within 4Å: Chain A: A.1011, A.1012, A.1020, C.1033 Ligands: MG.40 Ligand excluded by PLIP K.58: 4 residues within 4Å: Chain A: G.93, G.301, A.302, G.303 Ligand excluded by PLIP K.59: 4 residues within 4Å: Chain A: G.93, G.94, A.95, G.303 Ligand excluded by PLIP K.60: 6 residues within 4Å: Chain A: G.753, C.756, A.757, U.778, A.779, G.780 Ligand excluded by PLIP K.61: 5 residues within 4Å: Chain A: A.540, C.541, U.542, G.543, G.544 Ligand excluded by PLIP K.62: 5 residues within 4Å: Chain A: G.11, U.12, G.21, G.22, C.23 Ligand excluded by PLIP K.63: 5 residues within 4Å: Chain A: C.349, U.352, G.353, U.364, A.366 Ligand excluded by PLIP K.64: 7 residues within 4Å: Chain A: G.390, A.391, A.392, U.403, U.404, G.405 Ligands: MG.43 Ligand excluded by PLIP K.65: 5 residues within 4Å: Chain A: C.896, G.897, G.899, U.902, U.903 Ligand excluded by PLIP K.66: 2 residues within 4Å: Chain A: A.837, C.838 Ligand excluded by PLIP K.67: 6 residues within 4Å: Chain A: G.1023, U.1024, A.1025, U.1034, G.1035, C.1036 Ligand excluded by PLIP K.68: 6 residues within 4Å: Chain A: G.61, U.62, C.63, G.90, G.91 Chain N: K.9 Ligand excluded by PLIP K.69: 4 residues within 4Å: Chain A: G.101, A.102, G.103, G.266 Ligand excluded by PLIP K.70: 3 residues within 4Å: Chain A: G.270, U.281, G.282 Ligand excluded by PLIP K.71: 4 residues within 4Å: Chain A: C.291, A.292, U.294, G.295 Ligand excluded by PLIP K.72: 5 residues within 4Å: Chain A: G.857, G.858, G.859, C.882, U.883 Ligand excluded by PLIP K.73: 5 residues within 4Å: Chain A: G.228, U.229, G.243, U.245 Chain L: K.69 Ligand excluded by PLIP K.74: 3 residues within 4Å: Chain A: U.233, G.234, G.243 Ligand excluded by PLIP K.75: 5 residues within 4Å: Chain A: A.95, C.96, G.97, G.98, C.307 Ligand excluded by PLIP K.76: 5 residues within 4Å: Chain A: C.495, C.505, G.506 Chain I: P.45, N.46 Ligand excluded by PLIP K.77: 3 residues within 4Å: Chain A: G.866, G.867, U.876 Ligand excluded by PLIP K.78: 7 residues within 4Å: Chain A: U.5 Chain B: A.79, A.80, L.82, G.84, T.86, N.89 Ligand excluded by PLIP K.79: 3 residues within 4Å: Chain D: F.78, R.79, V.84 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Safdari, H.A. et al., The translation inhibitors kasugamycin, edeine and GE81112 target distinct steps during 30S initiation complex formation. Nat Commun (2025)

Release Date

2025-03-19

Peptides

Small ribosomal subunit protein uS4: B
Small ribosomal subunit protein uS5: C
Small ribosomal subunit protein bS6, fully modified isoform: D
Small ribosomal subunit protein uS8: E
Translation initiation factor IF-1: F
Translation initiation factor IF-3: G
Small ribosomal subunit protein uS11: H
Small ribosomal subunit protein uS12: I
Small ribosomal subunit protein uS15: J
Small ribosomal subunit protein bS16: K
Small ribosomal subunit protein uS17: L
Small ribosomal subunit protein bS18: M
Small ribosomal subunit protein bS20: N
Small ribosomal subunit protein bS21: O

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
D

C
E

D
F

E
H

F
I

G
J

H
K

I
L

J
O

K
P

L
Q

M
R

N
T

O
U

Small ribosomal subunit protein uS4

Small ribosomal subunit protein uS5

Small ribosomal subunit protein bS6, fully modified isoform

Small ribosomal subunit protein uS8

Translation initiation factor IF-1

Translation initiation factor IF-3

Small ribosomal subunit protein uS11

Small ribosomal subunit protein uS12

Small ribosomal subunit protein uS15

Small ribosomal subunit protein bS16

Small ribosomal subunit protein uS17

Small ribosomal subunit protein bS18

Small ribosomal subunit protein bS20

Small ribosomal subunit protein bS21

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