5FDU

Crystal structure of the Metalnikowin I antimicrobial peptide bound to the Thermus thermophilus 70S ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.183

Literature

Macromolecules
Sequence Display for 5FDU

Classification: RIBOSOME

Total Structure Weight: 4368310.50


Macromolecule Entities
Molecule Chains Length Organism Details
50S ribosomal protein L2 1D, 2D 275 Thermus thermophilus Gene Name(s): rplB TTHA1689
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L3 1E, 2E 204 Thermus thermophilus Gene Name(s): rplC TTHA1692
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L4 1F, 2F 203 Thermus thermophilus Gene Name(s): rplD TTHA1691
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L5 1G, 2G 181 Thermus thermophilus Gene Name(s): rplE TTHA1680
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L6 1H, 2H 174 Thermus thermophilus Gene Name(s): rplF BVI061214_01035
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L9 1I, 2I 147 Thermus thermophilus Gene Name(s): rplI TTHA0242
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L13 1N, 2N 140 Thermus thermophilus Gene Name(s): rplM TTHA1465
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L14 1O, 2O 122 Thermus thermophilus Gene Name(s): rplN TTHA1682
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L15 1P, 2P 149 Thermus thermophilus Gene Name(s): rplO TTHA1673
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L16 1Q, 2Q 141 Thermus thermophilus Gene Name(s): rplP TTHA1685
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L17 1R, 2R 118 Thermus thermophilus Gene Name(s): rplQ rpl17 TTHA1663
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L18 1S, 2S 110 Thermus thermophilus Gene Name(s): rplR TTHA1676
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L19 1T, 2T 131 Thermus thermophilus Gene Name(s): rplS TTHA1031
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L20 1U, 2U 116 Thermus thermophilus Gene Name(s): rplT TTHA0553
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L21 1V, 2V 101 Thermus thermophilus Gene Name(s): rplU TTHA1783
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L22 1W, 2W 112 Thermus thermophilus Gene Name(s): rplV TTHA1687
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L23 1X, 2X 95 Thermus thermophilus Gene Name(s): rplW TTHA1690
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L24 1Y, 2Y 107 Thermus thermophilus Gene Name(s): rplX TTHA1681
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L25 1Z, 2Z 203 Thermus thermophilus Gene Name(s): rplY rpl25 rptL5 TTHA1589
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L27 10, 20 77 Thermus thermophilus Gene Name(s): rpmA TTHA1782
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L28 11, 21 97 Thermus thermophilus Gene Name(s): rpmB TTHA0042
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L29 12, 22 70 Thermus thermophilus Gene Name(s): rpmC TTHA1684
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L30 13, 23 59 Thermus thermophilus Gene Name(s): rpmD TTHA1674
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L31 14, 24 69 Thermus thermophilus Gene Name(s): rpmE TTHA1073
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L32 15, 25 59 Thermus thermophilus Gene Name(s): rpmF rpl32 TTHA0418
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L33 16, 26 53 Thermus thermophilus Gene Name(s): rpmG rpl33 TTHA0250
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L34 17, 27 48 Thermus thermophilus Gene Name(s): rpmH rpl34 TTHA0446
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L35 18, 28 64 Thermus thermophilus Gene Name(s): rpmI TTHA0552
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L36 19, 29 37 Thermus thermophilus Gene Name(s): rpmJ TTHA1668
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S2 1b, 2b 231 Thermus thermophilus Gene Name(s): rpsB rps2 TTHA0861
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S3 1c, 2c 206 Thermus thermophilus Gene Name(s): rpsC rps3 TTHA1686
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S4 1d, 2d 208 Thermus thermophilus Gene Name(s): rpsD rps4 TTHA1665
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S5 1e, 2e 148 Thermus thermophilus Gene Name(s): rpsE TTHA1675
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S6 1f, 2f 100 Thermus thermophilus Gene Name(s): rpsF TTHA0245
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S7 1g, 2g 155 Thermus thermophilus Gene Name(s): rpsG rps7 TTHA1696
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S8 1h, 2h 137 Thermus thermophilus Gene Name(s): rpsH BVI061214_01034
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S9 1i, 2i 127 Thermus thermophilus Gene Name(s): rpsI rps9 TTHA1464
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S10 1j, 2j 97 Thermus thermophilus Gene Name(s): rpsJ TTHA1693
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S11 1k, 2k 114 Thermus thermophilus Gene Name(s): rpsK rps11 TTHA1666
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S12 1l, 2l 122 Thermus thermophilus Gene Name(s): rpsL TTHA1697
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S13 1m, 2m 116 Thermus thermophilus Gene Name(s): rpsM rps13 TTHA1667
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S14 type Z 1n, 2n 60 Thermus thermophilus Gene Name(s): rpsZ rpsN BVI061214_01033
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S15 1o, 2o 88 Thermus thermophilus Gene Name(s): rpsO TTHA1138
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S16 1p, 2p 82 Thermus thermophilus Gene Name(s): rpsP TTHA1035
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S17 1q, 2q 99 Thermus thermophilus Gene Name(s): rpsQ BVI061214_01029
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S18 1r, 2r 68 Thermus thermophilus Gene Name(s): rpsR TTHA0243
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S19 1s, 2s 83 Thermus thermophilus Gene Name(s): rpsS TTHA1688
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S20 1t, 2t 98 Thermus thermophilus Gene Name(s): rpsT rps20 TTHA1397
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein Thx 1u, 2u 23 Thermus thermophilus EC#: 4.1.1.3 IUBMB
Gene Name(s): rpsU TTHA1396
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ribosome-associated inhibitor A 1x, 2x 97 Escherichia coli Gene Name(s): raiA yfiA b2597 JW2578
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Metalnikowin I 1y, 2y 10 Palomena prasina
Macromolecule Entities
Molecule Chains Length Organism Details
23S ribosomal RNA 1A, 2A 2915 Thermus thermophilus
5S ribosomal RNA 1B, 2B 120 Thermus thermophilus
16S ribosomal RNA 1a, 2a 1521 Thermus thermophilus

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SF4
Query on SF4

1d, 2d IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
A
Query on A

1B, 2A ADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

14, 15, 16, 19, 1Y, 1n, 24, 25, 26, 29, 2Y, 2n ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

10, 11, 13, 15, 17, 18, 19, 1A, 1B, 1D, 1E, 1F, 1G, 1H, 1N, 1P, 1Q, 1R, 1S, 1T, 1U, 1V, 1W, 1X, 1Y, 1a, 1b, 1d, 1e, 1f, 1g, 1h, 1k, 1l, 1m, 1n, 1o, 1t, 20, 21, 23, 25, 27, 28, 2A, 2B, 2D, 2E, 2F, 2G, 2H, 2N, 2P, 2Q, 2R, 2S, 2T, 2U, 2V, 2W, 2X, 2a, 2b, 2d, 2e, 2f, 2g, 2h, 2l, 2m, 2n, 2o MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 13 Unique
ID Chains Type Formula 2D Diagram Parent
PSU
Query on PSU
1A, 1a, 2A, 2a RNA LINKING C9 H13 N2 O9 P U
5MU
Query on 5MU
1A, 2A RNA LINKING C10 H15 N2 O9 P U
4OC
Query on 4OC
1A, 1a, 2A, 2a RNA LINKING C11 H18 N3 O8 P C
5MC
Query on 5MC
1A, 1a, 2A, 2a RNA LINKING C10 H16 N3 O8 P C
OMG
Query on OMG
1A, 2A RNA LINKING C11 H16 N5 O8 P G
2MA
Query on 2MA
1A, 2A RNA LINKING C11 H16 N5 O7 P A
OMU
Query on OMU
1A, 2A RNA LINKING C10 H15 N2 O9 P U
7MG
Query on 7MG
1a, 2a RNA LINKING C11 H18 N5 O8 P G
M2G
Query on M2G
1a, 2a RNA LINKING C12 H18 N5 O8 P G
2MG
Query on 2MG
1a, 2a RNA LINKING C11 H16 N5 O8 P G
UR3
Query on UR3
1a, 2a RNA LINKING C10 H15 N2 O9 P U
MA6
Query on MA6
1a, 2a RNA LINKING C12 H18 N5 O7 P A
0TD
Query on 0TD
1l, 2l L-PEPTIDE LINKING C5 H9 N O4 S ASP

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.183
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 209.65 α = 90.00
b = 448.09 β = 90.00
c = 623.38 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2015-12-16
  • Released Date: 2016-01-27
  • Deposition author(s): Seefeldt, A.C., Graf, M., Perebaskine, N., Nguyen, F., Arenz, S., Mardirossian, M., Scocchi, M., Wilson, D.N., Innis, C.A.

Revision History

  • Version 1_0: 2016-01-27

    Type: Initial release

  • Version 1_1: 2016-02-03

    Type: Database references

  • Version 1_2: 2016-03-23

    Type: Structure summary

  • Version 1_3: 2016-03-30

    Type: Database references