4V8Q

COMPLEX OF SMPB, A TMRNA FRAGMENT AND EF-TU-GDP-KIRROMYCIN WITH THE 70S RIBOSOME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.270
  • R-Value Work: 0.230

Literature

Macromolecules
Sequence Display for 4V8Q

Classification: RIBOSOME

Total Structure Weight: 2348299.50


Macromolecule Entities
Molecule Chains Length Organism Details
50S RIBOSOMAL PROTEIN L27 A0 85 Thermus thermophilus Gene Name(s): rpmA TTHA1782
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L28 A1 98 Thermus thermophilus Gene Name(s): rpmB TTHA0042
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L29 A2 72 Thermus thermophilus Gene Name(s): rpmC TTHA1684
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L30 A3 60 Thermus thermophilus Gene Name(s): rpmD TTHA1674
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L31 A4 71 Thermus thermophilus Gene Name(s): rpmE TTHA1073
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L32 A5 60 Thermus thermophilus Gene Name(s): rpmF rpl32 TTHA0418
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L33 A6 54 Thermus thermophilus Gene Name(s): rpmG rpl33 TTHA0250
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L34 A7 49 Thermus thermophilus Gene Name(s): rpmH rpl34 TTHA0446
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L35 A8 65 Thermus thermophilus Gene Name(s): rpmI TTHA0552
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L36 A9 37 Thermus thermophilus Gene Name(s): rpmJ TTHA1668
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L1 AC 229 Thermus thermophilus Mutation: V19I, R27H, L127M
Gene Name(s): rplA TTHA0246
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L2 AD 276 Thermus thermophilus Gene Name(s): rplB TTHA1689
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L3 AE 206 Thermus thermophilus Gene Name(s): rplC TTHA1692
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L4 AF 210 Thermus thermophilus Gene Name(s): rplD TTHA1691
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L5 AG 182 Thermus thermophilus Gene Name(s): rplE TTHA1680
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L6 AH 180 Thermus thermophilus Gene Name(s): rplF TTHA1677
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L10 AJ 130 Thermus thermophilus Details: RESIDUES 4-133 ARE BUILT AS POLY-ALA
50S RIBOSOMAL PROTEIN L11 AK 140 Thermus thermophilus Details: BUILT AS POLY-ALA
50S RIBOSOMAL PROTEIN L13 AN 140 Thermus thermophilus Gene Name(s): rplM TTHA1465
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L14 AO 122 Thermus thermophilus Gene Name(s): rplN TTHA1682
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L15 AP 150 Thermus thermophilus Gene Name(s): rplO TTHA1673
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L16 AQ 141 Thermus thermophilus Gene Name(s): rplP TTHA1685
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L17 AR 118 Thermus thermophilus Gene Name(s): rplQ rpl17 TTHA1663
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L18 AS 112 Thermus thermophilus Gene Name(s): rplR TTHA1676
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L19 AT 146 Thermus thermophilus Gene Name(s): rplS TTHA1031
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L20 AU 118 Thermus thermophilus Gene Name(s): rplT TTHA0553
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L21 AV 101 Thermus thermophilus Gene Name(s): rplU TTHA1783
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L22 AW 113 Thermus thermophilus Gene Name(s): rplV TTHA1687
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L23 AX 96 Thermus thermophilus Gene Name(s): rplW TTHA1690
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L24 AY 110 Thermus thermophilus Gene Name(s): rplX TTHA1681
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L25 AZ 206 Thermus thermophilus Gene Name(s): rplY rpl25 rptL5 TTHA1589
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
SMALL PROTEIN B SMPB B2 144 Thermus thermophilus Details: PURIFIED USING RECOMBINANT TECHNIQUES
Gene Name(s): smpB TTHA0902
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S2 BB 256 Thermus thermophilus Gene Name(s): rpsB rps2 TTHA0861
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S3 BC 239 Thermus thermophilus Gene Name(s): rpsC rps3 TTHA1686
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S4 BD 209 Thermus thermophilus Gene Name(s): rpsD rps4 TTHA1665
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S5 BE 162 Thermus thermophilus Gene Name(s): rpsE TTHA1675
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S6 BF 101 Thermus thermophilus Gene Name(s): rpsF TTHA0245
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S7 BG 156 Thermus thermophilus Gene Name(s): rpsG rps7 TTHA1696
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S8 BH 138 Thermus thermophilus Gene Name(s): rpsH TTHA1678
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S9 BI 128 Thermus thermophilus Gene Name(s): rpsI rps9 TTHA1464
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S10 BJ 105 Thermus thermophilus Gene Name(s): rpsJ TTHA1693
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S11 BK 129 Thermus thermophilus Gene Name(s): rpsK rps11 TTHA1666
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S12 BL 135 Thermus thermophilus Gene Name(s): rpsL TTHA1697
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S13 BM 126 Thermus thermophilus Gene Name(s): rpsM rps13 TTHA1667
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S14 BN 61 Thermus thermophilus Gene Name(s): rpsZ rpsN TTHA1679
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S15 BO 89 Thermus thermophilus Gene Name(s): rpsO TTHA1138
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S16 BP 88 Thermus thermophilus Gene Name(s): rpsP TTHA1035
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S17 BQ 105 Thermus thermophilus Gene Name(s): rpsQ TTHA1683
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S18 BR 88 Thermus thermophilus Gene Name(s): rpsR TTHA0243
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S19 BS 93 Thermus thermophilus Gene Name(s): rpsS TTHA1688
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S20 BT 106 Thermus thermophilus Gene Name(s): rpsT rps20 TTHA1397
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN THX BU 27 Thermus thermophilus EC#: 4.1.1.3 IUBMB
Gene Name(s): rpsU TTHA1396
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ELONGATION FACTOR TU BZ 405 Thermus thermophilus Mutation: Q181E, R184K, R189K, R264K, V288L, V322I, S336T, Q354R, P357Q
Details: PURIFIED USING RECOMBINANT TECHNIQUES
Gene Name(s): tufA tuf TTHA1694
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
23S RIBOSOMAL RNA AA 2915 Thermus thermophilus CHAIN A (23S RNA) HAS E.COLI RESIDUE NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E. COLI STRUCTURE IN 2AW4
5S RIBOSOMAL RNA AB 122 Thermus thermophilus
16S RRNA BA 1522 Thermus thermophilus CHAIN A (16S RNA) HAS E.COLI NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E.COLI STRUCTURE IN 2AVY.
E-SITE TRNA FMET OR P-SITE TRNA FMET BV, BW 77 Escherichia coli
MRNA BX 19 Escherichia coli SEQUENCE GGCAAGGAGGUAA AAUGU A ONLY THE AAUGU SEQUENCE NEAR THE 3-END WAS ORDERED.
TMRNA DELA BY 90 Thermus thermophilus TMRNA DELTA 89 NT LONG. CENTRAL SEGMENT DISORDERED AND NOT PART OF THE PDB FILE.

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
KIR
Query on KIR

BZ KIRROMYCIN
MOCIMYCIN; DELVOMYCIN; MYC-8003 (Synonym)
C43 H60 N2 O12
HMSYAPGFKGSXAJ-PAHGNTJYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GDP
Query on GDP

BZ GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A9, BD, BN ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

AA, BZ MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
UNK
Query on UNK
AJ, AK L-PEPTIDE LINKING C4 H9 N O2 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.270
  • R-Value Work: 0.230
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 202.17 α = 90.00
b = 290.76 β = 97.63
c = 250.65 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2011-12-10
  • Released Date: 2014-07-09
  • Deposition author(s): Neubauer, C., Gillet, R., Kelley, A.C., Ramakrishnan, V.
  • Previous versions: 4ABR 4ABS

Revision History

  • 2014-12-10
    Type: Other