1M1K

Co-crystal structure of azithromycin bound to the 50S ribosomal subunit of Haloarcula marismortui

Structural Biology Knowledgebase: 1M1K SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.214

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1M1K

Classification: RIBOSOME

Total Structure Weight: 1458910.24


Macromolecule Entities
Molecule Chains Length Organism Details
RIBOSOMAL PROTEIN L2 C 239 Haloarcula marismortui Gene Name(s): rpl2 rrnAC1608
RIBOSOMAL PROTEIN L3 D 337 Haloarcula marismortui Mutation: ΔP310, F310R
Gene Name(s): rpl3 rrnAC1611
RIBOSOMAL PROTEIN L4 E 246 Haloarcula marismortui Gene Name(s): rpl4 rrnAC1610
RIBOSOMAL PROTEIN L5 F 176 Haloarcula marismortui Gene Name(s): rpl5 rrnAC1598
RIBOSOMAL PROTEIN L6 G 177 Haloarcula marismortui Gene Name(s): rpl6 rrnAC1596
RIBOSOMAL PROTEIN L7AE H 119 Haloarcula marismortui Gene Name(s): rpl7ae rrnAC0103
RIBOSOMAL PROTEIN L10 I 348 Haloarcula marismortui Gene Name(s): rpl10 rpl10e rplP0 rrnAC1417
RIBOSOMAL PROTEIN L10E J 167 Haloarcula marismortui Gene Name(s): rpl10e rrnAC2357
RIBOSOMAL PROTEIN L13 K 145 Haloarcula marismortui Gene Name(s): rpl13 rrnAC0065
RIBOSOMAL PROTEIN L14 L 132 Haloarcula marismortui Gene Name(s): rpl14 rrnAC1602
RIBOSOMAL PROTEIN L15 M 164 Haloarcula marismortui Gene Name(s): rpl15 rrnAC1590
RIBOSOMAL PROTEIN L15E N 194 Haloarcula marismortui Gene Name(s): rpl15e rrnAC2065
RIBOSOMAL PROTEIN L18 O 186 Haloarcula marismortui Gene Name(s): rpl18 rrnAC1593
RIBOSOMAL PROTEIN L18E P 115 Haloarcula marismortui Gene Name(s): rpl18e rrnAC0064
RIBOSOMAL PROTEIN L19E Q 148 Haloarcula marismortui Mutation: Y71K
Gene Name(s): rpl19e rrnAC1594
RIBOSOMAL PROTEIN L21E R 95 Haloarcula marismortui Gene Name(s): rpl21e rrnAC0260
RIBOSOMAL PROTEIN L22 S 154 Haloarcula marismortui Gene Name(s): rpl22 rrnAC1606
RIBOSOMAL PROTEIN L23 T 84 Haloarcula marismortui Gene Name(s): rpl23p rrnAC1609
RIBOSOMAL PROTEIN L24 U 119 Haloarcula marismortui Gene Name(s): rpl24p rrnAC1601
RIBOSOMAL PROTEIN L24E V 66 Haloarcula marismortui Gene Name(s): rpl24e rrnAC0104
RIBOSOMAL PROTEIN L29 W 70 Haloarcula marismortui Gene Name(s): rpl29p rrnAC1604
RIBOSOMAL PROTEIN L30 X 154 Haloarcula marismortui Gene Name(s): rpl30p rrnAC1591
RIBOSOMAL PROTEIN L31E Y 91 Haloarcula marismortui Gene Name(s): rpl31e rrnAC3113
RIBOSOMAL PROTEIN L32E Z 240 Haloarcula marismortui Gene Name(s): rpl32e rrnAC1595
RIBOSOMAL PROTEIN L37Ae 1 73 Haloarcula marismortui Gene Name(s): rpl37ae rrnAC1669
RIBOSOMAL PROTEIN L37E 2 56 Haloarcula marismortui Gene Name(s): rpl37e rrnAC0797.1
RIBOSOMAL PROTEIN L39E 3 48 Haloarcula marismortui Mutation: ΔR31
Gene Name(s): rpl39e rrnAC3112
RIBOSOMAL PROTEIN L44E 4 92 Haloarcula marismortui Gene Name(s): rpl44e rrnAC3514
Macromolecule Entities
Molecule Chains Length Organism Details
23S RRNA A 2922 Haloarcula marismortui
5S RRNA B 122 Haloarcula marismortui

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

A AZITHROMYCIN
C38 H72 N2 O12
MQTOSJVFKKJCRP-BICOPXKESA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CD
Query on CD

1, 2, 4, P, V CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

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

4, A, C, D, K, L, N, O, P, R, S CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

1, 4, A, B, C, D, L, U, Z MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B, C, E, J, K, M, N, R, S, T, U SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.214
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 213.75 α = 90.00
b = 301.57 β = 90.00
c = 574.44 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-06-19
  • Released Date: 2002-07-19
  • Deposition author(s): Hansen, J.L., Ippolito, J.A., Ban, N., Nissen, P., Moore, P.B., Steitz, T.A.

Revision History

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