Brand  (β version)

PDB ID: 1VQL

Hetero Atom Contents

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Color scheme of protein:

Ligands
Code Name Style Show Link
CD Cadmium ion PoSSuM
CL Chloride ion PoSSuM
K Potassium ion PoSSuM
MG Magnesium ion PoSSuM
NA Sodium ion PoSSuM
SR Strontium ion PoSSuM
Non-standard Residues
Code Name Show
1MA 6-hydro-1-methyladenosine-5'-monophosphate
OMG O2'-methylguanosine-5'-monophosphate
OMU O2'-methyluridine 5'-monophosphate
PPU Puromycin-5'-monophosphate
PSU Pseudouridine-5'-monophosphate
UR3 3-methyluridine-5'-monophoshate
Glycosylation
Code Name Emphasize
Modification
Code Name Show
TSE Thiophosphonoacetic acid

Structure summary

Code : 1VQL   PDBj   RCSB PDB   PDBe
Header : RIBOSOME
Title : The structure of the transition state analogue "DCSN" bound to the large ribosomal subunit of haloarcula marismortui
Release Data : 2005-11-29
Compound :
mol_id molecule chains
1 23S ribosomal rna 0
mol_id molecule chains
2 5S ribosomal RNA 9
mol_id molecule chains
3 5'-R(*CP*CP*(PPU)*(TSE)*(DA)*CP*C)-3' 4
mol_id molecule chains
4 50S ribosomal protein L2P A
mol_id molecule chains
5 50S ribosomal protein L3P B
mol_id molecule chains
6 50S ribosomal protein L4E C
mol_id molecule chains
7 50S ribosomal protein L5P D
mol_id molecule chains
8 50S ribosomal protein L6P E
mol_id molecule chains
9 50S ribosomal protein L7AE F
mol_id molecule chains
10 ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG G
mol_id molecule chains
11 50S RIBOSOMAL PROTEIN L10E H
mol_id molecule chains
12 50S ribosomal protein L13P J
mol_id molecule chains
13 50S ribosomal protein L14P K
mol_id molecule chains
14 50S ribosomal protein L15P L
mol_id molecule chains
15 50S Ribosomal Protein L15E M
mol_id molecule chains
16 50S ribosomal protein L18P N
mol_id molecule chains
17 50S ribosomal protein L18e O
mol_id molecule chains
18 50S ribosomal protein L19E P
mol_id molecule chains
19 50S ribosomal protein L21e Q
mol_id molecule chains
20 50S ribosomal protein L22P R
mol_id molecule chains
21 50S ribosomal protein L23P S
mol_id molecule chains
22 50S ribosomal protein L24P T
mol_id molecule chains
23 50S ribosomal protein L24E U
mol_id molecule chains
24 50S ribosomal protein L29P V
mol_id molecule chains
25 50S ribosomal protein L30P W
mol_id molecule chains
26 50S ribosomal protein L31e X
mol_id molecule chains
27 50S ribosomal protein L32E Y
mol_id molecule chains
28 50S ribosomal protein L37Ae Z
mol_id molecule chains
29 50S ribosomal protein L37e 1
mol_id molecule chains
30 50S ribosomal protein L39e 2
mol_id molecule chains
31 50S ribosomal protein L44E 3
mol_id molecule chains
32 50S RIBOSOMAL PROTEIN L11P I
Source :
mol_id organism_scientific
1 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
2 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
3
synthetic: yes
other_details: Synthetic oligo C-C-Puromycin- P=S-(CH2-CO2)-dA-C-C
mol_id organism_scientific
4 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
5 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
6 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
7 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
8 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
9 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
10 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
11 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
12 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
13 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
14 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
15 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
16 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
17 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
18 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
19 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
20 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
21 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
22 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
23 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
24 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
25 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
26 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
27 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
28 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
29 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
30 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
31 Haloarcula marismortui  (taxid:2238)
mol_id organism_scientific
32 Haloarcula marismortui  (taxid:2238)
Authors : Schmeing, T.M., Steitz, T.A.
Keywords : ribosome 50S, PROTEIN-PROTEIN COMPLEX, RNA-RNA COMPLEX, PROTEIN-RNA COMPLEX, PEPTIDYL TRANSFERASE REACTION, RIBOSOME
Exp. method : X-RAY DIFFRACTION ( 2.3 Å )
Citation :

Structural Insights into the Roles of Water and the 2' Hydroxyl of the P Site tRNA in the Peptidyl Transferase Reaction.

Schmeing, T.M.,Huang, K.S.,Kitchen, D.E.  et al.
(2005)  Mol.Cell  20 : 437 - 448

PubMed: 16285925
DOI: 10.1016/j.molcel.2005.09.006

Reaction

Chain : A
UniProt : P20276 (RL2_HALMA)
Reaction : -
Chain : C
UniProt : P12735 (RL4_HALMA)
Reaction : -
Chain : D
UniProt : P14124 (RL5_HALMA)
Reaction : -
Chain : E
UniProt : P14135 (RL6_HALMA)
Reaction : -
Chain : F
UniProt : P12743 (RL7A_HALMA)
Reaction : -
Chain : G
UniProt : P15825 (RL10_HALMA)
Reaction : -
Chain : J
UniProt : P29198 (RL13_HALMA)
Reaction : -
Chain : K
UniProt : P22450 (RL14_HALMA)
Reaction : -
Chain : L
UniProt : P12737 (RL15_HALMA)
Reaction : -
Chain : N
UniProt : P14123 (RL18_HALMA)
Reaction : -
Chain : O
UniProt : P12733 (RL18E_HALMA)
Reaction : -
Chain : P
UniProt : P14119 (RL19E_HALMA)
Reaction : -
Chain : Q
UniProt : P12734 (RL21_HALMA)
Reaction : -
Chain : R
UniProt : P10970 (RL22_HALMA)
Reaction : -
Chain : S
UniProt : P12732 (RL23_HALMA)
Reaction : -
Chain : T
UniProt : P10972 (RL24_HALMA)
Reaction : -
Chain : U
UniProt : P14116 (RL24E_HALMA)
Reaction : -
Chain : V
UniProt : P10971 (RL29_HALMA)
Reaction : -
Chain : W
UniProt : P14121 (RL30_HALMA)
Reaction : -
Chain : X
UniProt : P18138 (RL31_HALMA)
Reaction : -
Chain : Y
UniProt : P12736 (RL32_HALMA)
Reaction : -
Chain : 1
UniProt : P32410 (RL37_HALMA)
Reaction : -
Chain : 2
UniProt : P22452 (RL39_HALMA)
Reaction : -
Chain : 3
UniProt : P32411 (RL44E_HALMA)
Reaction : -