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Specific features and methylation sites of a plant ribosome. 40S head ribosomal subunit.
Analyse Specific features and methylation sites of a plant ribosome. 40S head ribosomal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QIY
- Type
- protein + RNA
- Length
- 2,221 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 18S rRNA head; Kh type-2 domain-containing protein; RIBOSOMAL_S7 domain-containing…
- EC
- 2.7.11.24
- UniProt
- A0A3Q7HBR5, A0A3Q7IVL4, A0A3Q7JYM3, A0A3Q7F5X2, A0A3Q7GDB0, P49215, A0A3Q7FJL7, A0A3Q7FTS1, A0A3Q7EMX2, K4B4Z0, A0A1U7V0A7, A0A3Q7GX91, A0A3Q7F3F2
- Ligands
- PUT, BGC, MG, K, ZN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 16 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 2 | 18S rRNA head | rna | 474 | — | — |
| D | Kh type-2 domain-containing protein | protein | 213 | 38% helix, 29% strand | A0A3Q7HBR5 |
| E | RIBOSOMAL_S7 domain-containing protein | protein | 185 | 53% helix, 8% strand | A0A3Q7IVL4 |
| F | S10_PLECTIN domain-containing protein | protein | 92 | 43% helix, 21% strand | A0A3Q7JYM3 |
| G | 40S head ribosomal protein US19 | protein | 126 | 37% helix, 15% strand | A0A3Q7F5X2 |
| H | 40S head ribosomal protein US9 | protein | 140 | 41% helix, 21% strand | A0A3Q7GDB0 |
| I | 40S ribosomal protein S17 | protein | 82 | 67% helix, 2% strand | P49215 |
| J | 40S head ribosomal protein US13 | protein | 142 | 45% helix, 9% strand | A0A3Q7FJL7 |
| K | 40S head ribosomal protein ES19 | protein | 140 | 47% helix, 13% strand | A0A3Q7FTS1 |
| L | RIBOSOMAL_S10 domain-containing protein | protein | 104 | 23% helix, 45% strand | A0A3Q7EMX2 |
| M | 40S head ribosomal protein ES28 | protein | 64 | 0% helix, 48% strand | K4B4Z0 |
| N | 40S ribosomal protein S29 | protein | 50 | 28% helix, 10% strand | A0A1U7V0A7 |
| O | Mitogen-activated protein kinase (EC 2.7.11.24) | protein | 317 | 2% helix, 50% strand | A0A3Q7GX91 |
| P | 40S ribosomal protein S25 | protein | 75 | 44% helix, 20% strand | A0A3Q7F3F2 |
| Q | TRNA | rna | 14 | — | — |
| R | MRNA | rna | 3 | — | — |
Ligands and binding sites
- PUT · 1,4-diaminobutane · ligand · chains 2
- BGC · beta-D-glucopyranose · sugar · chains D
- MG · Magnesium ion · metal · 28 copies · chains 2, H, D, K, J
- K · Potassium ion · metal · 10 copies · chains 2, L, J, K, N
- ZN · Zinc ion · metal · chains 2, 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 | 659 | 0.85 | 0.90 | 68 | empty |
| 2 | 707 | 0.85 | 0.90 | 60 | PUT, MG |
| 3 | 384 | 0.84 | 0.94 | 55 | MG, K |
| 4 | 398 | 0.84 | 0.93 | 55 | MG |
| 5 | 1104 | 0.83 | 0.85 | 85 | MG |
Interfaces
37 interfaces between chains.
- 2–H · 3016 Ų buried · 78 hydrogen bonds · protein-nucleic
- 2–K · 2807 Ų buried · 74 hydrogen bonds · protein-nucleic
- 2–J · 2287 Ų buried · 68 hydrogen bonds · protein-nucleic
- 2–G · 2052 Ų buried · 57 hydrogen bonds · protein-nucleic
- 2–E · 1816 Ų buried · 43 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 27 modified, 1 glycan (nucleotide modification, glycosylation).
Compared structures
- 7QIY · Specific features and methylation sites of a plant ribosome. 40S head ribosomal subunit. · the same entry in another collection · chain R against R, 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 A0A3Q7HBR5
- Every structure of UniProt A0A3Q7IVL4
- Every structure of UniProt A0A3Q7JYM3
- Every structure of UniProt A0A3Q7F5X2
- Every structure of UniProt A0A3Q7GDB0
- Every structure of UniProt P49215
- Every structure of UniProt A0A3Q7FJL7
- Every structure of UniProt A0A3Q7FTS1
- Every structure of UniProt A0A3Q7EMX2
- Every structure of UniProt K4B4Z0
- Every structure of UniProt A0A1U7V0A7
- Every structure of UniProt A0A3Q7GX91
- Every structure of UniProt A0A3Q7F3F2
- Elsewhere: RCSB PDB 7QIY · PDBe 7QIY · UniProt A0A3Q7HBR5 · UniProt A0A3Q7IVL4 · UniProt A0A3Q7JYM3 · UniProt A0A3Q7F5X2 · UniProt A0A3Q7GDB0 · UniProt P49215 · UniProt A0A3Q7FJL7 · UniProt A0A3Q7FTS1 · UniProt A0A3Q7EMX2 · UniProt K4B4Z0 · UniProt A0A1U7V0A7 · UniProt A0A3Q7GX91 · UniProt A0A3Q7F3F2
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