1VQ6

The structure of c-hpmn and CCA-PHE-CAP-BIO bound to the large ribosomal subunit of haloarcula marismortui

Structural Biology Knowledgebase: 1VQ6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.193

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1VQ6

Classification: RIBOSOME

Total Structure Weight: 1481693.35


Macromolecule Entities
Molecule Chains Length Organism Details
50S ribosomal protein L2P A 240 Haloarcula marismortui Gene Name(s): rpl2 rrnAC1608
50S ribosomal protein L3P B 338 Haloarcula marismortui Gene Name(s): rpl3 rrnAC1611
50S ribosomal protein L4E C 246 Haloarcula marismortui Gene Name(s): rpl4 rrnAC1610
50S ribosomal protein L5P D 177 Haloarcula marismortui Gene Name(s): rpl5 rrnAC1598
50S ribosomal protein L6P E 178 Haloarcula marismortui Gene Name(s): rpl6 rrnAC1596
50S ribosomal protein L7AE F 120 Haloarcula marismortui Gene Name(s): rpl7ae rrnAC0103
ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG G 348 Haloarcula marismortui Gene Name(s): rpl10 rpl10e rplP0 rrnAC1417
50S RIBOSOMAL PROTEIN L10E H 171 Haloarcula marismortui Gene Name(s): rpl10e rrnAC2357
50S ribosomal protein L13P J 145 Haloarcula marismortui Gene Name(s): rpl13 rrnAC0065
50S ribosomal protein L14P K 132 Haloarcula marismortui Mutation: H44L
Gene Name(s): rpl14 rrnAC1602
50S ribosomal protein L15P L 165 Haloarcula marismortui Gene Name(s): rpl15 rrnAC1590
50S Ribosomal Protein L15E M 194 Haloarcula marismortui Mutation: K13E, G194A
Gene Name(s): rpl15e rrnAC2065
50S ribosomal protein L18P N 187 Haloarcula marismortui Gene Name(s): rpl18 rrnAC1593
50S ribosomal protein L18e O 116 Haloarcula marismortui Gene Name(s): rpl18e rrnAC0064
50S ribosomal protein L19E P 149 Haloarcula marismortui Gene Name(s): rpl19e rrnAC1594
50S ribosomal protein L21e Q 96 Haloarcula marismortui Gene Name(s): rpl21e rrnAC0260
50S ribosomal protein L22P R 155 Haloarcula marismortui Gene Name(s): rpl22 rrnAC1606
50S ribosomal protein L23P S 85 Haloarcula marismortui Gene Name(s): rpl23p rrnAC1609
50S ribosomal protein L24P T 120 Haloarcula marismortui Gene Name(s): rpl24p rrnAC1601
50S ribosomal protein L24E U 66 Haloarcula marismortui Gene Name(s): rpl24e rrnAC0104
50S ribosomal protein L29P V 71 Haloarcula marismortui Gene Name(s): rpl29p rrnAC1604
50S ribosomal protein L30P W 154 Haloarcula marismortui Gene Name(s): rpl30p rrnAC1591
50S ribosomal protein L31e X 92 Haloarcula marismortui Gene Name(s): rpl31e rrnAC3113
50S ribosomal protein L32E Y 241 Haloarcula marismortui Gene Name(s): rpl32e rrnAC1595
50S ribosomal protein L37Ae Z 83 Haloarcula marismortui Mutation: S10R
Gene Name(s): rpl37ae rrnAC1669
50S ribosomal protein L37e 1 57 Haloarcula marismortui Gene Name(s): rpl37e rrnAC0797.1
50S ribosomal protein L39e 2 50 Haloarcula marismortui Gene Name(s): rpl39e rrnAC3112
50S ribosomal protein L44E 3 92 Haloarcula marismortui Gene Name(s): rpl44e rrnAC3514
50S RIBOSOMAL PROTEIN L11P I 162 Haloarcula marismortui Gene Name(s): rpl11 rrnAC1414
Macromolecule Entities
Molecule Chains Length Organism Details
23S ribosomal rna 0 2922 Haloarcula marismortui
5S ribosomal RNA 9 122 Haloarcula marismortui
5'-R(*CP*(5AA)*(HFA))-3' 4 3 synthetic
5'-R(*CP*CP*AP*(PHE)*(ACA)*(BTN))-3' 5 6 synthetic

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CD
Query on CD

1, 3, O, U, Z CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

0 POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

0, 3, A, B, J, K, L, M, N, O, R, Y CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

0, 3, 5, 9, A, B, K, T, Y MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

0, 9, A, C, H, J, L, M, Q, R, S SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 9 Unique
ID Chains Type Formula 2D Diagram Parent
1MA
Query on 1MA
0 RNA LINKING C11 H16 N5 O7 P A
OMU
Query on OMU
0 RNA LINKING C10 H15 N2 O9 P U
OMG
Query on OMG
0 RNA LINKING C11 H16 N5 O8 P G
UR3
Query on UR3
0 RNA LINKING C10 H15 N2 O9 P U
PSU
Query on PSU
0 RNA LINKING C9 H13 N2 O9 P U
5AA
Query on 5AA
4 RNA LINKING C12 H19 N6 O6 P DA
HFA
Query on HFA
4 L-PEPTIDE LINKING C9 H10 O3 --
ACA
Query on ACA
5 PEPTIDE LINKING C6 H13 N O2 --
BTN
Query on BTN
5 NON-POLYMER C10 H16 N2 O3 S --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.193
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 212.05 α = 90.00
b = 300.19 β = 90.00
c = 573.99 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-12-16
  • Released Date: 2005-11-29
  • Deposition author(s): Schmeing, T.M., Steitz, T.A.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update