MolNFT v1 · #136629 · protein + RNA
The cryo-EM structure of yjeq bound to the 30S subunit suggests a fidelity checkpoint function for this protein in ribosome assembly
5UZ4 · 16S ribosomal RNA: “The cryo-EM structure of yjeq bound to the 30S subunit suggests a fidelity checkpoint function for this…”. Electron microscopy, 2 ligands (GGM, ZN), 20 pockets (best druggability 0.88). MolNFT v1 #136629 on…
- PDB
- 5UZ4
- Type
- protein + RNA
- Length
- 4,156 residues
- Chains
- 21
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S ribosomal RNA; 30S ribosomal protein S3; 30S ribosomal protein S4; 30S ribosomal…
- EC
- 3.6.1.-
- UniProt
- B7MCS9, B7MCR2, P0A7W3, P02358, P02359, B7MCS1, B7MBZ1, B7MCT6, B7MCR3, B7MCV7, P0A7T1, B7MCS2, Q8X9M2, B7MIU7, B7MCS6, B7MLK7, B7MCT1, B7MAE3, B7MBF0, P39286
- Ligands
- GGM, ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 21 distinct chains · 33% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S ribosomal RNA | rna | 1527 | — | — |
| C | 30S ribosomal protein S3 | protein | 206 | 33% helix, 20% strand | B7MCS9 |
| D | 30S ribosomal protein S4 | protein | 205 | 40% helix, 7% strand | B7MCR2 |
| E | 30S ribosomal protein S5 | protein | 150 | 25% helix, 34% strand | P0A7W3 |
| F | 30S ribosomal protein S6 | protein | 100 | 28% helix, 37% strand | P02358 |
| G | 30S ribosomal protein S7 | protein | 149 | 46% helix, 5% strand | P02359 |
| H | 30S ribosomal protein S8 | protein | 129 | 29% helix, 23% strand | B7MCS1 |
| I | 30S ribosomal protein S9 | protein | 127 | 24% helix, 19% strand | B7MBZ1 |
| J | 30S ribosomal protein S10 | protein | 98 | 14% helix, 23% strand | B7MCT6 |
| K | 30S ribosomal protein S11 | protein | 116 | 17% helix, 30% strand | B7MCR3 |
| L | 30S ribosomal protein S12 | protein | 123 | 4% helix, 22% strand | B7MCV7 |
| M | 30S ribosomal protein S13 | protein | 109 | 44% helix, 2% strand | P0A7T1 |
| N | 30S ribosomal protein S14 | protein | 98 | 35% helix, 6% strand | B7MCS2 |
| O | 30S ribosomal protein S15 | protein | 86 | 74% helix, 0% strand | Q8X9M2 |
| P | 30S ribosomal protein S16 | protein | 82 | 22% helix, 23% strand | B7MIU7 |
| Q | 30S ribosomal protein S17 | protein | 80 | 0% helix, 39% strand | B7MCS6 |
| R | 30S ribosomal protein S18 | protein | 51 | 51% helix, 0% strand | B7MLK7 |
| S | 30S ribosomal protein S19 | protein | 79 | 20% helix, 15% strand | B7MCT1 |
| T | 30S ribosomal protein S20 | protein | 85 | 80% helix, 0% strand | B7MAE3 |
| B | 30S ribosomal protein S2 | protein | 233 | 50% helix, 13% strand | B7MBF0 |
| Z | Small ribosomal subunit biogenesis GTPase rsga (EC 3.6.1.-) | protein | 323 | 28% helix, 20% strand | P39286 |
Ligands and binding sites
- GGM · 3'-O-(N-methylanthraniloyl)-beta:gamma-imidoguanosine-5'-triphosphate · ligand · chains Z
- ZN · Zinc ion · metal · chains Z
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 | 973 | 0.88 | 0.90 | 119 | empty |
| 2 | 1154 | 0.86 | 0.88 | 98 | empty |
| 3 | 1044 | 0.85 | 0.87 | 69 | empty |
| 4 | 960 | 0.84 | 0.86 | 104 | GGM |
| 5 | 673 | 0.83 | 0.89 | 58 | empty |
Interfaces
40 interfaces between chains.
- A–D · 3159 Ų buried · 131 hydrogen bonds · protein-nucleic
- A–I · 3087 Ų buried · 103 hydrogen bonds · protein-nucleic
- A–L · 2882 Ų buried · 95 hydrogen bonds · protein-nucleic
- A–T · 2366 Ų buried · 76 hydrogen bonds · protein-nucleic
- A–G · 2196 Ų buried · 75 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 5UZ4 · The cryo-EM structure of YjeQ bound to the 30S subunit suggests a fidelity checkpoint… · the same entry in another collection · chain L against L, 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 B7MCS9
- Every structure of UniProt B7MCR2
- Every structure of UniProt P0A7W3
- Every structure of UniProt P02358
- Every structure of UniProt P02359
- Every structure of UniProt B7MCS1
- Every structure of UniProt B7MBZ1
- Every structure of UniProt B7MCT6
- Every structure of UniProt B7MCR3
- Every structure of UniProt B7MCV7
- Every structure of UniProt P0A7T1
- Every structure of UniProt B7MCS2
- Every structure of UniProt Q8X9M2
- Every structure of UniProt B7MIU7
- Every structure of UniProt B7MCS6
- Every structure of UniProt B7MLK7
- Every structure of UniProt B7MCT1
- Every structure of UniProt B7MAE3
- Every structure of UniProt B7MBF0
- Every structure of UniProt P39286
- Elsewhere: RCSB PDB 5UZ4 · PDBe 5UZ4 · UniProt B7MCS9 · UniProt B7MCR2 · UniProt P0A7W3 · UniProt P02358 · UniProt P02359 · UniProt B7MCS1 · UniProt B7MBZ1 · UniProt B7MCT6 · UniProt B7MCR3 · UniProt B7MCV7 · UniProt P0A7T1 · UniProt B7MCS2 · UniProt Q8X9M2 · UniProt B7MIU7 · UniProt B7MCS6 · UniProt B7MLK7 · UniProt B7MCT1 · UniProt B7MAE3 · UniProt B7MBF0 · UniProt P39286
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