30S Doxycycline Bound E. coli Ribosome
Stuart, W.S., Isupov, M.N., McLaren, M., Jenkins, C.H., Monier, A., Daum, B., Norville, I.H., Gold, V.A.M., Harmer, N.J.To be published.
Experimental Data Snapshot
Starting Model: experimental
View more details
wwPDB Validation 3D Report Full Report
Macromolecule Content 
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Large ribosomal subunit protein bL31 | A [auth 4] | 67 | Escherichia coli BL21(DE3) | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C3SIV2 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Small ribosomal subunit protein uS2 | C [auth B] | 241 | Escherichia coli BL21(DE3) | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C3TPN2 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Small ribosomal subunit protein uS3 | D [auth C] | 233 | Escherichia coli BL21(DE3) | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C3SQX2 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Small ribosomal subunit protein uS4 | E [auth D] | 206 | Escherichia coli BL21(DE3) | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C3SR62 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 6 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Small ribosomal subunit protein uS5 | F [auth E] | 167 | Escherichia coli BL21(DE3) | Mutation(s): 0  | ![]() |
UniProt | |||||
Find proteins for A0A090BZW5 (Escherichia coli) Explore A0A090BZW5  Go to UniProtKB:  A0A090BZW5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A090BZW5 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 7 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Small ribosomal subunit protein bS6 | G [auth F] | 131 | Escherichia coli BL21(DE3) | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | W8T6F0 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 8 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Small ribosomal subunit protein uS7 | H [auth G] | 156 | Escherichia coli BL21(DE3) | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C3SQS2 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 9 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Small ribosomal subunit protein uS8 | I [auth H] | 130 | Escherichia coli BL21(DE3) | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C3SR12 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 10 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Small ribosomal subunit protein uS9 | J [auth I] | 130 | Escherichia coli BL21(DE3) | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C3SRY2 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 11 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Small ribosomal subunit protein uS12 | K [auth L] | 124 | Escherichia coli BL21(DE3) | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C3SQR7 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 12 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Small ribosomal subunit protein uS13 | L [auth M] | 118 | Escherichia coli BL21(DE3) | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C3SR52 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 13 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Small ribosomal subunit protein uS14 | M [auth N] | 101 | Escherichia coli BL21(DE3) | Mutation(s): 0  | ![]() |
UniProt | |||||
Find proteins for A0A2X1PQW4 (Escherichia coli) Explore A0A2X1PQW4  Go to UniProtKB:  A0A2X1PQW4 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A2X1PQW4 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 14 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Small ribosomal subunit protein uS15 | N [auth O] | 89 | Escherichia coli BL21(DE3) | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C3SSQ7 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 15 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Small ribosomal subunit protein bS16 | O [auth P] | 82 | Escherichia coli BL21(DE3) | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C3SYP2 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 16 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Small ribosomal subunit protein uS17 | P [auth Q] | 84 | Escherichia coli BL21(DE3) | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C3SQY7 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 17 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Small ribosomal subunit protein bS18 | Q [auth R] | 75 | Escherichia coli BL21(DE3) | Mutation(s): 0  | ![]() |
Entity ID: 18 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Small ribosomal subunit protein uS19 | R [auth S] | 92 | Escherichia coli BL21(DE3) | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C3SQW2 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 19 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Small ribosomal subunit protein bS20 | S [auth T] | 87 | Escherichia coli BL21(DE3) | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C3TRH7 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 20 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Small ribosomal subunit protein bS21 | T [auth U] | 71 | Escherichia coli BL21(DE3) | Mutation(s): 0  | ![]() |
UniProt | |||||
Find proteins for A0A6I7DAD8 (Proteus columbae) Explore A0A6I7DAD8  Go to UniProtKB:  A0A6I7DAD8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A6I7DAD8 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 21 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Small ribosomal subunit protein uS11 | U [auth K] | 129 | Escherichia coli BL21(DE3) | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C3SR57 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 22 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Small ribosomal subunit protein uS10 | V [auth J] | 103 | Escherichia coli BL21(DE3) | Mutation(s): 0  | ![]() |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C3SQT7 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Entity ID: 2 | ||||
| Molecule | Chains | Length | Organism | Image |
|---|---|---|---|---|
| 16S ribosomal RNA | B [auth A] | 1,534 | Escherichia coli BL21(DE3) | ![]() |
Sequence AnnotationsExpand | ||||
Reference Sequence | ||||
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| DXT (Subject of Investigation/LOI) Download:Ideal Coordinates CCD File | X [auth A] | (4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE C22 H24 N2 O8 JBIWCJUYHHGXTC-AKNGSSGZSA-N | |||
| ZN Download:Ideal Coordinates CCD File | W [auth 4] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
| K Download:Ideal Coordinates CCD File | IF [auth A], JF [auth A], KF [auth A], LF [auth A] | POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N | |||
| MG Download:Ideal Coordinates CCD File | AA [auth A] AB [auth A] AC [auth A] AD [auth A] AE [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N | |||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| D2T Query on D2T | K [auth L] | L-PEPTIDE LINKING | C5 H9 N O4 S | ASP | |
| Task | Software Package | Version |
|---|---|---|
| RECONSTRUCTION | cryoSPARC | 4 |
| MODEL REFINEMENT | REFMAC |
| Funding Organization | Location | Grant Number |
|---|---|---|
| Biotechnology and Biological Sciences Research Council (BBSRC) | United Kingdom | BB/M009122/1 |