3G71

Co-crystal structure of Bruceantin bound to the large ribosomal subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.186

Literature

Macromolecules
Sequence Display for 3G71

Classification: RIBOSOME

Total Structure Weight: 1461630.50


Macromolecule Entities
Molecule Chains Length Organism Details
50S ribosomal protein L2P A 237 Haloarcula marismortui Fragment: Residues 143-264
Gene Name(s): rpl2 rrnAC1608
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L3P B 337 Haloarcula marismortui Gene Name(s): rpl3 rrnAC1611
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L4P C 246 Haloarcula marismortui Gene Name(s): rpl4 rrnAC1610
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L5P D 177 Haloarcula marismortui Gene Name(s): rpl5 rrnAC1598
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L6P E 172 Haloarcula marismortui Gene Name(s): rpl6 rrnAC1596
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L7Ae F 119 Haloarcula marismortui Gene Name(s): rpl7ae rrnAC0103
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L10E G 348 Haloarcula marismortui Gene Name(s): rpl10 rpl10e rplP0 rrnAC1417
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L10e H 177 Haloarcula marismortui Gene Name(s): rpl10e rrnAC2357
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L11P I 70 Haloarcula marismortui Gene Name(s): rpl11 rrnAC1414
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L13P J 142 Haloarcula marismortui Gene Name(s): rpl13 rrnAC0065
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L14P K 132 Haloarcula marismortui Gene Name(s): rpl14 rrnAC1602
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L15P L 165 Haloarcula marismortui Gene Name(s): rpl15 rrnAC1590
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L15e M 194 Haloarcula marismortui Gene Name(s): rpl15e rrnAC2065
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L18P N 186 Haloarcula marismortui Gene Name(s): rpl18 rrnAC1593
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L18e O 115 Haloarcula marismortui Gene Name(s): rpl18e rrnAC0064
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L19e P 143 Haloarcula marismortui Gene Name(s): rpl19e rrnAC1594
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L21e Q 95 Haloarcula marismortui Gene Name(s): rpl21e rrnAC0260
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L22P R 150 Haloarcula marismortui Gene Name(s): rpl22 rrnAC1606
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L23P S 81 Haloarcula marismortui Gene Name(s): rpl23p rrnAC1609
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L24P T 119 Haloarcula marismortui Gene Name(s): rpl24p rrnAC1601
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L24e U 53 Haloarcula marismortui Gene Name(s): rpl24e rrnAC0104
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L29P V 65 Haloarcula marismortui Gene Name(s): rpl29p rrnAC1604
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L30P W 154 Haloarcula marismortui Gene Name(s): rpl30p rrnAC1591
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L31e X 82 Haloarcula marismortui Gene Name(s): rpl31e rrnAC3113
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L32e Y 142 Haloarcula marismortui Gene Name(s): rpl32e rrnAC1595
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L37Ae Z 73 Haloarcula marismortui Gene Name(s): rpl37ae rrnAC1669
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L37e 1 56 Haloarcula marismortui Gene Name(s): rpl37e rrnAC0797.1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L39e 2 50 Haloarcula marismortui Gene Name(s): rpl39e rrnAC3112
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L44E 3 92 Haloarcula marismortui Gene Name(s): rpl44e rrnAC3514
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
23S ribosomal RNA 0 2923 Haloarcula marismortui
5S ribosomal RNA 9 122 Haloarcula marismortui

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
WIN
Query on WIN

0 methyl (5beta,7alpha,9beta,10alpha,11alpha,12alpha,13beta,15alpha)- 15-{[(2E)-3,4-dimethylpent-2-enoyl]oxy}-3,11,12- trihydroxy-2,16-dioxo-13,20-epoxypicras-3- en-21-oate
11,, (11beta,12alpha (Synonym)
C28 H36 O11
IRQXZTBHNKVIRL-GOTQHHPNSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CD
Query on CD

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

0, 1, 3, 9, A, B, F, R, S STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

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

0, 2, 9, A, B, K, T, Y MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

0, 9, C, H, J, M, Q, R, S SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 5 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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.186
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 212.21 α = 90.00
b = 299.54 β = 90.00
c = 574.25 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-02-09
  • Released Date: 2009-04-28
  • Deposition author(s): Gurel, G., Blaha, G., Moore, P.B., Steitz, T.A.

Revision History

  • Version 1_0: 2009-04-28

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Non-polymer description, Version format compliance

  • Version 1_2: 2015-03-18

    Type: Structure summary