Research workbench
Structure of dimeric escherichia COLI toxin yoeb bound to the thermus thermophilus 30S ribosome
Analyse Structure of dimeric escherichia COLI toxin yoeb bound to the thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NY6
- Type
- protein + RNA
- Length
- 4,058 residues
- Chains
- 23
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S rRNA; 30S ribosomal protein S2; 30S ribosomal protein S3; 30S ribosomal protein S4…
- UniProt
- P80371, P80372, P80373, Q5SHQ5, Q5SLP8, P17291, P0DOY9, P80374, Q5SHN7, P80376, Q5SHN3, P80377, P0DOY6, Q5SJ76, Q5SJH3, P0DOY7, Q5SLQ0, Q5SHP2, P80380, Q5SIH3, A0A127GIW6
- Ligands
- SF4, MG, ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 22 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S rRNA | rna | 1513 | — | — |
| B | 30S ribosomal protein S2 | protein | 236 | 40% helix, 12% strand | P80371 |
| C | 30S ribosomal protein S3 | protein | 205 | 37% helix, 29% strand | P80372 |
| D | 30S ribosomal protein S4 | protein | 208 | 43% helix, 10% strand | P80373 |
| E | 30S ribosomal protein S5 | protein | 151 | 30% helix, 40% strand | Q5SHQ5 |
| F | 30S ribosomal protein S6 | protein | 100 | 25% helix, 49% strand | Q5SLP8 |
| G | 30S ribosomal protein S7 | protein | 155 | 55% helix, 10% strand | P17291 |
| H | 30S ribosomal protein S8 | protein | 137 | 26% helix, 30% strand | P0DOY9 |
| I | 30S ribosomal protein S9 | protein | 126 | 25% helix, 20% strand | P80374 |
| J | 30S ribosomal protein S10 | protein | 96 | 19% helix, 23% strand | Q5SHN7 |
| K | 30S ribosomal protein S11 | protein | 116 | 32% helix, 28% strand | P80376 |
| L | 30S ribosomal protein S12 | protein | 122 | 7% helix, 24% strand | Q5SHN3 |
| M | 30S ribosomal protein S13 | protein | 116 | 49% helix, 2% strand | P80377 |
| N | 30S ribosomal protein S14 type Z | protein | 60 | 25% helix, 5% strand | P0DOY6 |
| O | 30S ribosomal protein S15 | protein | 87 | 74% helix, 0% strand | Q5SJ76 |
| P | 30S ribosomal protein S16 | protein | 84 | 23% helix, 35% strand | Q5SJH3 |
| Q | 30S ribosomal protein S17 | protein | 100 | 14% helix, 53% strand | P0DOY7 |
| R | 30S ribosomal protein S18 | protein | 70 | 44% helix, 9% strand | Q5SLQ0 |
| S | 30S ribosomal protein S19 | protein | 84 | 18% helix, 18% strand | Q5SHP2 |
| T | 30S ribosomal protein S20 | protein | 99 | 68% helix, 0% strand | P80380 |
| U | 30S ribosomal protein thx | protein | 25 | 28% helix, 0% strand | Q5SIH3 |
| Y, Z | Toxin yoeb | protein | 84 | 31% helix, 26% strand | A0A127GIW6 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains D
- MG · Magnesium ion · metal · 184 copies · chains A, K, N, U, L, M, C, E, T, D, B
- ZN · Zinc ion · metal · chains N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.86 | 0.88 | 116 | MG |
| 2 | 665 | 0.85 | 0.90 | 76 | MG |
| 3 | 1012 | 0.85 | 0.87 | 87 | MG |
| 4 | 1017 | 0.85 | 0.87 | 79 | MG |
| 5 | 511 | 0.84 | 0.92 | 45 | MG |
Interfaces
46 interfaces between chains.
- A–D · 3200 Ų buried · 104 hydrogen bonds · protein-nucleic
- A–L · 3167 Ų buried · 79 hydrogen bonds · protein-nucleic
- A–I · 3126 Ų buried · 101 hydrogen bonds · protein-nucleic
- A–Q · 2789 Ų buried · 61 hydrogen bonds · protein-nucleic
- A–T · 2675 Ų buried · 57 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified, 1 disulfide (nucleotide modification, disulfide).
Compared structures
- 6NY6 · Structure of dimeric Escherichia coli toxin YoeB bound to the Thermus thermophilus 30S… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P80371
- Every structure of UniProt P80372
- Every structure of UniProt P80373
- Every structure of UniProt Q5SHQ5
- Every structure of UniProt Q5SLP8
- Every structure of UniProt P17291
- Every structure of UniProt P0DOY9
- Every structure of UniProt P80374
- Every structure of UniProt Q5SHN7
- Every structure of UniProt P80376
- Every structure of UniProt Q5SHN3
- Every structure of UniProt P80377
- Every structure of UniProt P0DOY6
- Every structure of UniProt Q5SJ76
- Every structure of UniProt Q5SJH3
- Every structure of UniProt P0DOY7
- Every structure of UniProt Q5SLQ0
- Every structure of UniProt Q5SHP2
- Every structure of UniProt P80380
- Every structure of UniProt Q5SIH3
- Every structure of UniProt A0A127GIW6
- Elsewhere: RCSB PDB 6NY6 · PDBe 6NY6 · UniProt P80371 · UniProt P80372 · UniProt P80373 · UniProt Q5SHQ5 · UniProt Q5SLP8 · UniProt P17291 · UniProt P0DOY9 · UniProt P80374 · UniProt Q5SHN7 · UniProt P80376 · UniProt Q5SHN3 · UniProt P80377 · UniProt P0DOY6 · UniProt Q5SJ76 · UniProt Q5SJH3 · UniProt P0DOY7 · UniProt Q5SLQ0 · UniProt Q5SHP2 · UniProt P80380 · UniProt Q5SIH3 · UniProt A0A127GIW6
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