SMTL ID : 8wq4.1

Structural basis of translation inhibition by a valine tRNA-derived fragment

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

57 x UNL: UNKNOWN LIGAND(Non-functional Binders)

UNL.1: 6 residues within 4Å: Chain A: A.830 Ligands: UNL.2, UNL.14, UNL.15, UNL.51, UNL.57 Ligand excluded by PLIP UNL.2: 8 residues within 4Å: Chain A: C.829, A.830 Ligands: UNL.1, UNL.3, UNL.14, UNL.15, UNL.16, UNL.57 Ligand excluded by PLIP UNL.3: 7 residues within 4Å: Chain 1: R.17 Chain A: A.794, C.829 Ligands: UNL.2, UNL.15, UNL.16, UNL.17 Ligand excluded by PLIP UNL.4: 4 residues within 4Å: Ligands: UNL.43, UNL.44, UNL.45, UNL.46 Ligand excluded by PLIP UNL.5: 5 residues within 4Å: Chain C: G.131, I.132 Ligands: UNL.6, UNL.7, UNL.47 Ligand excluded by PLIP UNL.6: 5 residues within 4Å: Chain C: G.131 Ligands: UNL.5, UNL.7, UNL.11, UNL.12 Ligand excluded by PLIP UNL.7: 5 residues within 4Å: Ligands: UNL.5, UNL.6, UNL.8, UNL.48, UNL.49 Ligand excluded by PLIP UNL.8: 4 residues within 4Å: Chain C: R.58 Ligands: UNL.7, UNL.9, UNL.10 Ligand excluded by PLIP UNL.9: 3 residues within 4Å: Chain C: R.58 Ligands: UNL.8, UNL.10 Ligand excluded by PLIP UNL.10: 3 residues within 4Å: Ligands: UNL.8, UNL.9, UNL.48 Ligand excluded by PLIP UNL.11: 3 residues within 4Å: Ligands: UNL.6, UNL.12, UNL.50 Ligand excluded by PLIP UNL.12: 5 residues within 4Å: Ligands: UNL.6, UNL.11, UNL.13, UNL.50, UNL.53 Ligand excluded by PLIP UNL.13: 7 residues within 4Å: Chain C: F.146 Ligands: UNL.12, UNL.14, UNL.15, UNL.37, UNL.51, UNL.53 Ligand excluded by PLIP UNL.14: 6 residues within 4Å: Ligands: UNL.1, UNL.2, UNL.13, UNL.15, UNL.51, UNL.57 Ligand excluded by PLIP UNL.15: 9 residues within 4Å: Chain C: D.145, F.146 Ligands: UNL.1, UNL.2, UNL.3, UNL.13, UNL.14, UNL.18, UNL.57 Ligand excluded by PLIP UNL.16: 6 residues within 4Å: Chain A: A.794 Chain C: Y.24, R.143 Ligands: UNL.2, UNL.3, UNL.17 Ligand excluded by PLIP UNL.17: 5 residues within 4Å: Chain C: Y.24 Ligands: UNL.3, UNL.16, UNL.18, UNL.19 Ligand excluded by PLIP UNL.18: 5 residues within 4Å: Ligands: UNL.15, UNL.17, UNL.19, UNL.20, UNL.57 Ligand excluded by PLIP UNL.19: 4 residues within 4Å: Ligands: UNL.17, UNL.18, UNL.20, UNL.21 Ligand excluded by PLIP UNL.20: 4 residues within 4Å: Ligands: UNL.18, UNL.19, UNL.21, UNL.22 Ligand excluded by PLIP UNL.21: 5 residues within 4Å: Ligands: UNL.19, UNL.20, UNL.22, UNL.23, UNL.24 Ligand excluded by PLIP UNL.22: 4 residues within 4Å: Ligands: UNL.20, UNL.21, UNL.23, UNL.24 Ligand excluded by PLIP UNL.23: 4 residues within 4Å: Ligands: UNL.21, UNL.22, UNL.24, UNL.52 Ligand excluded by PLIP UNL.24: 6 residues within 4Å: Ligands: UNL.21, UNL.22, UNL.23, UNL.25, UNL.26, UNL.52 Ligand excluded by PLIP UNL.25: 6 residues within 4Å: Ligands: UNL.24, UNL.26, UNL.27, UNL.28, UNL.29, UNL.52 Ligand excluded by PLIP UNL.26: 5 residues within 4Å: Ligands: UNL.24, UNL.25, UNL.27, UNL.28, UNL.52 Ligand excluded by PLIP UNL.27: 4 residues within 4Å: Ligands: UNL.25, UNL.26, UNL.28, UNL.29 Ligand excluded by PLIP UNL.28: 5 residues within 4Å: Ligands: UNL.25, UNL.26, UNL.27, UNL.29, UNL.30 Ligand excluded by PLIP UNL.29: 5 residues within 4Å: Ligands: UNL.25, UNL.27, UNL.28, UNL.30, UNL.31 Ligand excluded by PLIP UNL.30: 5 residues within 4Å: Chain C: K.54, R.58 Ligands: UNL.28, UNL.29, UNL.31 Ligand excluded by PLIP UNL.31: 4 residues within 4Å: Chain C: K.54, F.55 Ligands: UNL.29, UNL.30 Ligand excluded by PLIP UNL.32: 6 residues within 4Å: Chain F: K.22, F.25, E.26, Y.192, K.204 Ligands: UNL.33 Ligand excluded by PLIP UNL.33: 5 residues within 4Å: Chain F: Y.192, K.204 Ligands: UNL.32, UNL.34, UNL.42 Ligand excluded by PLIP UNL.34: 8 residues within 4Å: Chain F: R.108, Y.192, M.203, K.204 Ligands: UNL.33, UNL.35, UNL.40, UNL.42 Ligand excluded by PLIP UNL.35: 7 residues within 4Å: Chain F: M.203 Ligands: UNL.34, UNL.36, UNL.39, UNL.40, UNL.41, UNL.42 Ligand excluded by PLIP UNL.36: 6 residues within 4Å: Chain F: R.202 Ligands: UNL.35, UNL.37, UNL.39, UNL.40, UNL.56 Ligand excluded by PLIP UNL.37: 5 residues within 4Å: Chain F: R.202 Ligands: UNL.13, UNL.36, UNL.38, UNL.53 Ligand excluded by PLIP UNL.38: 5 residues within 4Å: Chain F: R.202 Ligands: UNL.37, UNL.53, UNL.54, UNL.55 Ligand excluded by PLIP UNL.39: 6 residues within 4Å: Chain F: R.193, V.195 Ligands: UNL.35, UNL.36, UNL.40, UNL.56 Ligand excluded by PLIP UNL.40: 6 residues within 4Å: Chain F: Y.192 Ligands: UNL.34, UNL.35, UNL.36, UNL.39, UNL.41 Ligand excluded by PLIP UNL.41: 6 residues within 4Å: Chain F: Y.189, Y.192 Ligands: UNL.35, UNL.40, UNL.42, UNL.43 Ligand excluded by PLIP UNL.42: 8 residues within 4Å: Chain F: F.25, N.28 Ligands: UNL.33, UNL.34, UNL.35, UNL.41, UNL.43, UNL.44 Ligand excluded by PLIP UNL.43: 6 residues within 4Å: Chain F: I.105 Ligands: UNL.4, UNL.41, UNL.42, UNL.44, UNL.45 Ligand excluded by PLIP UNL.44: 9 residues within 4Å: Chain F: F.25, N.28, L.29, P.30, I.31 Ligands: UNL.4, UNL.42, UNL.43, UNL.45 Ligand excluded by PLIP UNL.45: 3 residues within 4Å: Ligands: UNL.4, UNL.43, UNL.44 Ligand excluded by PLIP UNL.46: 4 residues within 4Å: Chain F: N.28, P.30 Ligands: UNL.4, UNL.47 Ligand excluded by PLIP UNL.47: 3 residues within 4Å: Chain F: N.28 Ligands: UNL.5, UNL.46 Ligand excluded by PLIP UNL.48: 4 residues within 4Å: Ligands: UNL.7, UNL.10, UNL.49, UNL.50 Ligand excluded by PLIP UNL.49: 3 residues within 4Å: Ligands: UNL.7, UNL.48, UNL.50 Ligand excluded by PLIP UNL.50: 5 residues within 4Å: Chain F: M.203 Ligands: UNL.11, UNL.12, UNL.48, UNL.49 Ligand excluded by PLIP UNL.51: 4 residues within 4Å: Ligands: UNL.1, UNL.13, UNL.14, UNL.57 Ligand excluded by PLIP UNL.52: 4 residues within 4Å: Ligands: UNL.23, UNL.24, UNL.25, UNL.26 Ligand excluded by PLIP UNL.53: 7 residues within 4Å: Chain 1: K.20 Ligands: UNL.12, UNL.13, UNL.37, UNL.38, UNL.54, UNL.55 Ligand excluded by PLIP UNL.54: 7 residues within 4Å: Chain 1: R.18, K.20 Ligands: UNL.38, UNL.53, UNL.55, UNL.56, UNL.57 Ligand excluded by PLIP UNL.55: 8 residues within 4Å: Chain 1: K.20, L.63, G.64, R.65 Ligands: UNL.38, UNL.53, UNL.54, UNL.56 Ligand excluded by PLIP UNL.56: 6 residues within 4Å: Chain 1: G.64, R.65 Ligands: UNL.36, UNL.39, UNL.54, UNL.55 Ligand excluded by PLIP UNL.57: 8 residues within 4Å: Chain 1: R.18 Ligands: UNL.1, UNL.2, UNL.14, UNL.15, UNL.18, UNL.51, UNL.54 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, Y. et al., Structural basis of translation inhibition by a valine tRNA-derived fragment. Life Sci Alliance (2024)

Release Date

2024-04-10

Peptides

30S ribosomal protein S2: C
30S ribosomal protein S4e: D
30S ribosomal protein S4: E
30S ribosomal protein S5: F
30S ribosomal protein S6e: G
30S ribosomal protein S8e: H
30S ribosomal protein S11: I
30S ribosomal protein S12: J
30S ribosomal protein S15: K
30S ribosomal protein S17: L
30S ribosomal protein S24e: M
30S ribosomal protein S27e: N
30S ribosomal protein S3Ae: O
30S ribosomal protein S3: P
30S ribosomal protein S7: Q
30S ribosomal protein S9: R
30S ribosomal protein S10: S
30S ribosomal protein S13: T
30S ribosomal protein S14 type Z: U
30S ribosomal protein S17e: V
30S ribosomal protein S19e: W
30S ribosomal protein S19: X
30S ribosomal protein S27ae: Y
30S ribosomal protein S28e: Z
50S ribosomal protein L7Ae: 0
Small ribosomal subunit protein uS8: 1

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
AS2P

D
AS4E

E
AS4P

F
AS5P

G
AS6E

H
AS8E

I
S11P

J
S12P

K
S15P

L
S17P

M
S24E

N
S27E

O
S3AE

P
AS3P

Q
AS7P

R
AS9P

S
S10P

T
S13P

U
S14P

V
S17E

W
S19E

X
S19P

Y
S27A

Z
S28E

0
SL7A

1
AS8P

30S ribosomal protein S2

30S ribosomal protein S4e

30S ribosomal protein S4

30S ribosomal protein S5

30S ribosomal protein S6e

30S ribosomal protein S8e

30S ribosomal protein S11

30S ribosomal protein S12

30S ribosomal protein S15

30S ribosomal protein S17

30S ribosomal protein S24e

30S ribosomal protein S27e

30S ribosomal protein S3Ae

30S ribosomal protein S3

30S ribosomal protein S7

30S ribosomal protein S9

30S ribosomal protein S10

30S ribosomal protein S13

30S ribosomal protein S14 type Z

30S ribosomal protein S17e

30S ribosomal protein S19e

30S ribosomal protein S19

30S ribosomal protein S27ae

30S ribosomal protein S28e

50S ribosomal protein L7Ae

Small ribosomal subunit protein uS8

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