1KQS

The Haloarcula marismortui 50S Complexed with a Pretranslocational Intermediate in Protein Synthesis

Structural Biology Knowledgebase: 1KQS SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.220
  • R-Value Work: 0.173

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1KQS

Classification: RIBOSOME

Total Structure Weight: 1460697.44


Macromolecule Entities
Molecule Chains Length Organism Details
RIBOSOMAL PROTEIN L2 A 239 Haloarcula marismortui Gene Name(s): rpl2 rrnAC1608
RIBOSOMAL PROTEIN L3 B 337 Haloarcula marismortui Mutation: ΔP310, F310R
Gene Name(s): rpl3 rrnAC1611
RIBOSOMAL PROTEIN L4 C 246 Haloarcula marismortui Gene Name(s): rpl4 rrnAC1610
RIBOSOMAL PROTEIN L5 D 176 Haloarcula marismortui Gene Name(s): rpl5 rrnAC1598
RIBOSOMAL PROTEIN L6 E 177 Haloarcula marismortui Gene Name(s): rpl6 rrnAC1596
RIBOSOMAL PROTEIN L7AE F 119 Haloarcula marismortui Gene Name(s): rpl7ae rrnAC0103
RIBOSOMAL PROTEIN L10 G 348 Haloarcula marismortui Gene Name(s): rpl10 rpl10e rplP0 rrnAC1417
RIBOSOMAL PROTEIN L10E H 167 Haloarcula marismortui Gene Name(s): rpl10e rrnAC2357
RIBOSOMAL PROTEIN L13 I 145 Haloarcula marismortui Gene Name(s): rpl13 rrnAC0065
RIBOSOMAL PROTEIN L14 J 132 Haloarcula marismortui Gene Name(s): rpl14 rrnAC1602
RIBOSOMAL PROTEIN L15 K 164 Haloarcula marismortui Gene Name(s): rpl15 rrnAC1590
RIBOSOMAL PROTEIN L15E L 194 Haloarcula marismortui Gene Name(s): rpl15e rrnAC2065
RIBOSOMAL PROTEIN L18 M 186 Haloarcula marismortui Gene Name(s): rpl18 rrnAC1593
RIBOSOMAL PROTEIN L18E N 115 Haloarcula marismortui Gene Name(s): rpl18e rrnAC0064
RIBOSOMAL PROTEIN L19E O 148 Haloarcula marismortui Mutation: Y71K
Gene Name(s): rpl19e rrnAC1594
RIBOSOMAL PROTEIN L21E P 95 Haloarcula marismortui Gene Name(s): rpl21e rrnAC0260
RIBOSOMAL PROTEIN L22 Q 154 Haloarcula marismortui Gene Name(s): rpl22 rrnAC1606
RIBOSOMAL PROTEIN L23 R 84 Haloarcula marismortui Gene Name(s): rpl23p rrnAC1609
RIBOSOMAL PROTEIN L24 S 119 Haloarcula marismortui Gene Name(s): rpl24p rrnAC1601
RIBOSOMAL PROTEIN L24E T 66 Haloarcula marismortui Gene Name(s): rpl24e rrnAC0104
RIBOSOMAL PROTEIN L29 U 70 Haloarcula marismortui Gene Name(s): rpl29p rrnAC1604
RIBOSOMAL PROTEIN L30 V 154 Haloarcula marismortui Gene Name(s): rpl30p rrnAC1591
RIBOSOMAL PROTEIN L31E W 91 Haloarcula marismortui Gene Name(s): rpl31e rrnAC3113
RIBOSOMAL PROTEIN L32E X 240 Haloarcula marismortui Gene Name(s): rpl32e rrnAC1595
RIBOSOMAL PROTEIN L37Ae Y 73 Haloarcula marismortui Gene Name(s): rpl37ae rrnAC1669
RIBOSOMAL PROTEIN L37E Z 56 Haloarcula marismortui Gene Name(s): rpl37e rrnAC0797.1
RIBOSOMAL PROTEIN L39E 1 48 Haloarcula marismortui Mutation: ΔR31
Gene Name(s): rpl39e rrnAC3112
RIBOSOMAL PROTEIN L44E 2 92 Haloarcula marismortui Gene Name(s): rpl44e rrnAC3514
Macromolecule Entities
Molecule Chains Length Organism Details
23S RRNA 0 2922 Haloarcula marismortui
5S RRNA 9 122 Haloarcula marismortui
CCA 3 3 synthetic RNA ANALOGUE OF 3' OF DEACYLATED-TRNA
CC-Pmn-pcb 4 2 synthetic AN ANALOGUE OF PEPTIDYL-TRNA CONTAINS PUROMYCIN-5'-MONOPHOSPHATE, PHENYLALANINAL, 6-AMINOHEXANOIC ACID, AND BIOTIN

Small Molecules
Ligands 9 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PPU
Query on PPU

4 PUROMYCIN-5'-MONOPHOSPHATE
C22 H30 N7 O8 P
NYICMZBLMICLBS-NVWDDTSBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BTN
Query on BTN

4 BIOTIN
C10 H16 N2 O3 S
YBJHBAHKTGYVGT-ZKWXMUAHSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PHA
Query on PHA

4 PHENYLALANINAL
C9 H11 N O
CQIUZHAQYHXKRY-VIFPVBQESA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACA
Query on ACA

4 6-AMINOHEXANOIC ACID
AMINOCAPROIC ACID (Synonym)
C6 H13 N O2
SLXKOJJOQWFEFD-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CD
Query on CD

2, N, T, Y, 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, 2, A, B, I, K, L, M, N, Q, X CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

0, 2, 9, A, J, S, X, Y MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

0, 9, A, C, H, I, K, L, P, Q, R SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.220
  • R-Value Work: 0.173
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 212.78 α = 90.00
b = 300.35 β = 90.00
c = 574.96 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-01-07
  • Released Date: 2002-02-22
  • Deposition author(s): Schmeing, T.M., Seila, A.C., Hansen, J.L., Freeborn, B., Soukup, J.K., Scaringe, S.A., Strobel, S.A., Moore, P.B., Steitz, T.A.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4