1YIT

Crystal Structure Of Virginiamycin M and S Bound To The 50S Ribosomal Subunit Of Haloarcula Marismortui


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.221
  • R-Value Work: 0.175

Literature

Macromolecules
Sequence Display for 1YIT

Classification: RIBOSOME / ANTIBIOTIC

Total Structure Weight: 1481914.38


Macromolecule Entities
Molecule Chains Length Organism Details
50S RIBOSOMAL PROTEIN L37E 1 57 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
VIRGINIAMYCIN S1 8 7 Streptomyces virginiae
50S RIBOSOMAL PROTEIN L2P A 240 Haloarcula marismortui Gene Name(s): rpl2 rrnAC1608
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L3P B 338 Haloarcula marismortui Gene Name(s): rpl3 rrnAC1611
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L4E 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 178 Haloarcula marismortui Gene Name(s): rpl6 rrnAC1596
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L7AE F 120 Haloarcula marismortui Gene Name(s): rpl7ae rrnAC0103
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG 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 162 Haloarcula marismortui Gene Name(s): rpl11 rrnAC1414
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L13P J 145 Haloarcula marismortui Gene Name(s): rpl13 rrnAC0065
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L14P K 132 Haloarcula marismortui Mutation: H44L
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 195 Haloarcula marismortui Mutation: K13E
Gene Name(s): rpl15e rrnAC2065
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L18P N 187 Haloarcula marismortui Gene Name(s): rpl18 rrnAC1593
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L18E O 116 Haloarcula marismortui Gene Name(s): rpl18e rrnAC0064
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L19E P 149 Haloarcula marismortui Gene Name(s): rpl19e rrnAC1594
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L21E Q 96 Haloarcula marismortui Gene Name(s): rpl21e rrnAC0260
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L22P R 155 Haloarcula marismortui Gene Name(s): rpl22 rrnAC1606
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L23P S 85 Haloarcula marismortui Gene Name(s): rpl23p rrnAC1609
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L24P T 120 Haloarcula marismortui Gene Name(s): rpl24p rrnAC1601
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L24E U 66 Haloarcula marismortui Gene Name(s): rpl24e rrnAC0104
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L29P V 71 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 92 Haloarcula marismortui Gene Name(s): rpl31e rrnAC3113
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L32E Y 241 Haloarcula marismortui Gene Name(s): rpl32e rrnAC1595
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L37AE Z 83 Haloarcula marismortui Mutation: S10R
Gene Name(s): rpl37ae rrnAC1669
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
23S RIBOSOMAL RNA 0 2922 Haloarcula marismortui ENCODED BY RRNA OPERON
5S RIBOSOMAL RNA 9 122 Haloarcula marismortui

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
VIR
Query on VIR

0 VIRGINIAMYCIN M1
C28 H35 N3 O7
DAIKHDNSXMZDCU-FQTGFAPKSA-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)
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, 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, 3, 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, A, C, H, J, L, M, Q, R, S SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000227
Query on PRD_000227
8 VIRGINIAMYCIN S1 Cyclic peptide /
Antibiotic, Antimicrobial
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (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: 2.8 Å
  • R-Value Free: 0.221
  • R-Value Work: 0.175
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 212.58 α = 90.00
b = 299.76 β = 90.00
c = 573.56 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-01-13
  • Released Date: 2005-04-26
  • Deposition author(s): Tu, D., Blaha, G., Moore, P.B., Steitz, T.A.

Revision History

  • Version 1_0: 2005-04-26

    Type: Initial release

  • Version 1_1: 2011-06-14

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance

  • Version 1_3: 2011-07-27

    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary

  • Version 1_4: 2012-12-12

    Type: Other