MolNFT v1 · #139214 · protein + RNA
Structure of the 30S small subunit of chloroplast ribosome from spinach
5X8R · 30S ribosomal protein S2, chloroplastic: “Structure of the 30S small subunit of chloroplast ribosome from spinach”. Electron microscopy, 20 pockets (best druggability 0.88). MolNFT v1 #139214 on GenesisL1: 3D structure, binding…
- PDB
- 5X8R
- Type
- protein + RNA
- Length
- 4,449 residues
- Chains
- 26
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 30S ribosomal protein S2, chloroplastic; 30S ribosomal protein S3, chloroplastic; 30S…
- UniProt
- P08242, P09595, Q9ST69, P82403, P82129, P09597, P82278, A0A0K9RWE7, P06506, P62128, P82163, Q9M3I4, P28807, A0A0K9RRR0, Q9M3K7, P06508, A0A0K9RHF9, A0A0K9QHQ6, A0A0K9RJX3, P13788, A0A0K9R1W7, P06507, A0A0K9RMU8, P29344
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 26 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| b | 30S ribosomal protein S2, chloroplastic | protein | 227 | 46% helix, 8% strand | P08242 |
| c | 30S ribosomal protein S3, chloroplastic | protein | 213 | 35% helix, 25% strand | P09595 |
| e | 30S ribosomal protein S5, chloroplastic | protein | 171 | 23% helix, 33% strand | Q9ST69 |
| f | 30S ribosomal protein S6 alpha, chloroplastic | protein | 111 | 19% helix, 32% strand | P82403 |
| g | 30S ribosomal protein S7, chloroplastic | protein | 149 | 53% helix, 7% strand | P82129 |
| h | 30S ribosomal protein S8, chloroplastic | protein | 134 | 24% helix, 25% strand | P09597 |
| i | 30S ribosomal protein S9, chloroplastic | protein | 133 | 32% helix, 17% strand | P82278 |
| j | Protein S10 | protein | 98 | 26% helix, 39% strand | A0A0K9RWE7 |
| k | 30S ribosomal protein S11, chloroplastic | protein | 118 | 22% helix, 28% strand | P06506 |
| l | 30S ribosomal protein S12, chloroplastic | protein | 123 | 0% helix, 26% strand | P62128 |
| m | 30S ribosomal protein S13, chloroplastic | protein | 110 | 45% helix, 2% strand | P82163 |
| o | 30S ribosomal protein S15, chloroplastic | protein | 62 | 79% helix, 0% strand | Q9M3I4 |
| p | 30S ribosomal protein S16, chloroplastic | protein | 80 | 24% helix, 20% strand | P28807 |
| q | Protein S17 | protein | 78 | 0% helix, 47% strand | A0A0K9RRR0 |
| r | 30S ribosomal protein S18, chloroplastic | protein | 64 | 31% helix, 3% strand | Q9M3K7 |
| s | 30S ribosomal protein S19 alpha, chloroplastic | protein | 78 | 21% helix, 14% strand | P06508 |
| t | Protein S20 | protein | 105 | 69% helix, 0% strand | — |
| u | Protein S21 | protein | 44 | 57% helix, 0% strand | A0A0K9RHF9 |
| y | Protein plastid py | protein | 108 | 33% helix, 29% strand | A0A0K9QHQ6 |
| a | 16S rRNA | rna | 1480 | — | — |
| w | Protein CS23 | protein | 84 | 39% helix, 19% strand | A0A0K9RJX3 |
| d | 30S ribosomal protein S4, chloroplastic | protein | 199 | 40% helix, 5% strand | P13788 |
| v | Protein CS22 | protein | 190 | 32% helix, 28% strand | A0A0K9R1W7 |
| n | 30S ribosomal protein S14, chloroplastic | protein | 99 | 38% helix, 1% strand | P06507 |
| x | Protein bthxc | protein | 37 | 19% helix, 0% strand | A0A0K9RMU8 |
| 8 | 30S ribosomal protein S1, chloroplastic | protein | 154 | 29% helix, 16% strand | P29344 |
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 | 941 | 0.88 | 0.90 | 86 | empty |
| 2 | 857 | 0.85 | 0.88 | 82 | empty |
| 3 | 980 | 0.85 | 0.87 | 76 | empty |
| 4 | 1031 | 0.85 | 0.87 | 80 | empty |
| 5 | 884 | 0.84 | 0.86 | 92 | empty |
Interfaces
55 interfaces between chains.
- l–a · 3122 Ų buried · 69 hydrogen bonds · protein-nucleic
- a–d · 3034 Ų buried · 61 hydrogen bonds · protein-nucleic
- i–a · 2930 Ų buried · 73 hydrogen bonds · protein-nucleic
- t–a · 2687 Ų buried · 59 hydrogen bonds · protein-nucleic
- b–8 · 2631 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 5X8R · Structure of the 30S small subunit of chloroplast ribosome from spinach · the same entry in another collection · chain k against k, 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 P08242
- Every structure of UniProt P09595
- Every structure of UniProt Q9ST69
- Every structure of UniProt P82403
- Every structure of UniProt P82129
- Every structure of UniProt P09597
- Every structure of UniProt P82278
- Every structure of UniProt A0A0K9RWE7
- Every structure of UniProt P06506
- Every structure of UniProt P62128
- Every structure of UniProt P82163
- Every structure of UniProt Q9M3I4
- Every structure of UniProt P28807
- Every structure of UniProt A0A0K9RRR0
- Every structure of UniProt Q9M3K7
- Every structure of UniProt P06508
- Every structure of UniProt A0A0K9RHF9
- Every structure of UniProt A0A0K9QHQ6
- Every structure of UniProt A0A0K9RJX3
- Every structure of UniProt P13788
- Every structure of UniProt A0A0K9R1W7
- Every structure of UniProt P06507
- Every structure of UniProt A0A0K9RMU8
- Every structure of UniProt P29344
- Elsewhere: RCSB PDB 5X8R · PDBe 5X8R · UniProt P08242 · UniProt P09595 · UniProt Q9ST69 · UniProt P82403 · UniProt P82129 · UniProt P09597 · UniProt P82278 · UniProt A0A0K9RWE7 · UniProt P06506 · UniProt P62128 · UniProt P82163 · UniProt Q9M3I4 · UniProt P28807 · UniProt A0A0K9RRR0 · UniProt Q9M3K7 · UniProt P06508 · UniProt A0A0K9RHF9 · UniProt A0A0K9QHQ6 · UniProt A0A0K9RJX3 · UniProt P13788 · UniProt A0A0K9R1W7 · UniProt P06507 · UniProt A0A0K9RMU8 · UniProt P29344
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