MolNFT v1 · #68226 · protein + RNA
Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome
3JD5 · 28S ribosomal RNA, mitochondial: “Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome”. Electron microscopy, 20 pockets (best druggability 0.89). MolNFT v1 #68226 on GenesisL1: 3D structure, binding sites…
- PDB
- 3JD5
- Type
- protein + RNA
- Length
- 6,435 residues
- Chains
- 33
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 28S ribosomal RNA, mitochondial; 28S ribosomal protein S2, mitochondrial; 28S ribosomal…
- UniProt
- P82923, Q2M2T7, Q2KID9, P82931, Q3T040, Q58DQ5, P82670, P82911, Q29RU1, Q6B860, E1BBB4, P82915, P82916, P82917, P82920, P82649, Q2NL27, P82669, Q3SZ86, Q32PI8, P82928, P82922, P82925, P82926, P82929, Q2YDF6, Q2HJE8, Q0VCJ1, Q2KI62, P82918
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 33 distinct chains · 37% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 28S ribosomal RNA, mitochondial | rna | 952 | — | — |
| B | 28S ribosomal protein S2, mitochondrial | protein | 217 | 34% helix, 13% strand | P82923 |
| C | 28S ribosomal protein S24, mitochondrial | protein | 132 | 28% helix, 17% strand | Q2M2T7 |
| E | 28S ribosomal protein S5, mitochondrial | protein | 328 | 24% helix, 17% strand | Q2KID9 |
| F | 28S ribosomal protein S6, mitochondrial | protein | 124 | 19% helix, 21% strand | P82931 |
| G | 28S ribosomal protein S7, mitochondrial | protein | 208 | 53% helix, 7% strand | Q3T040 |
| I | 28S ribosomal protein S9, mitochondrial | protein | 311 | 37% helix, 10% strand | Q58DQ5 |
| J | 28S ribosomal protein S10, mitochondrial | protein | 128 | 23% helix, 28% strand | P82670 |
| K | 28S ribosomal protein S11, mitochondrial | protein | 136 | 20% helix, 21% strand | P82911 |
| L | 28S ribosomal protein S12, mitochondrial | protein | 109 | 4% helix, 25% strand | Q29RU1 |
| N | 28S ribosomal protein S14, mitochondrial | protein | 101 | 44% helix, 3% strand | Q6B860 |
| O | 28S ribosomal protein S15, mitochondrial | protein | 173 | 59% helix, 1% strand | E1BBB4 |
| P | 28S ribosomal protein S16, mitochondrial | protein | 116 | 36% helix, 22% strand | P82915 |
| Q | 28S ribosomal protein S17, mitochondrial | protein | 109 | 0% helix, 40% strand | P82916 |
| R | 28S ribosomal protein S18C, mitochondrial | protein | 97 | 22% helix, 1% strand | P82917 |
| U | 28S ribosomal protein S21, mitochondrial | protein | 86 | 58% helix, 2% strand | P82920 |
| a | 28S ribosomal protein S22, mitochondrial | protein | 289 | 44% helix, 7% strand | P82649 |
| b | 28S ribosomal protein S23, mitochondrial | protein | 135 | 33% helix, 1% strand | Q2NL27 |
| c | 28S ribosomal protein S25, mitochondrial | protein | 168 | 31% helix, 13% strand | P82669 |
| d | 28S ribosomal protein S26, mitochondrial | protein | 176 | 69% helix, 2% strand | Q3SZ86 |
| e | 28S ribosomal protein S27, mitochondrial | protein | 344 | 46% helix, 1% strand | Q32PI8 |
| f | 28S ribosomal protein S28, mitochondrial | protein | 98 | 9% helix, 32% strand | P82928 |
| g | 28S ribosomal protein S29, mitochondrial | protein | 338 | 39% helix, 12% strand | P82922 |
| h | 28S ribosomal protein S31, mitochondrial | protein | 103 | 50% helix, 0% strand | P82925 |
| i | 28S ribosomal protein S33, mitochondrial | protein | 98 | 44% helix, 0% strand | P82926 |
| j | 28S ribosomal protein S34, mitochondrial | protein | 213 | 20% helix, 17% strand | P82929 |
| k | 28S ribosomal protein S35, mitochondrial | protein | 275 | 34% helix, 7% strand | Q2YDF6 |
| m | Coiled-coil-helix-coiled-coil-helix domain containing 1 | protein | 118 | 28% helix, 0% strand | Q2HJE8 |
| n | Aurora kinase a interacting protein 1 | protein | 72 | 64% helix, 0% strand | Q0VCJ1 |
| o | Pentatricopeptide repeat domain-containing protein 3, mitochondrial | protein | 461 | 55% helix, 0% strand | Q2KI62 |
| p | 28S ribosomal protein S18B, mitochondrial | protein | 187 | 24% helix, 2% strand | P82918 |
| s | Unknown | protein | 16 | 81% helix, 0% strand | — |
| z | Unknown | protein | 17 | 41% helix, 0% strand | — |
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 | 840 | 0.89 | 0.93 | 108 | empty |
| 2 | 1190 | 0.86 | 0.88 | 93 | empty |
| 3 | 1086 | 0.86 | 0.87 | 89 | empty |
| 4 | 909 | 0.85 | 0.87 | 66 | empty |
| 5 | 1180 | 0.84 | 0.85 | 72 | empty |
Interfaces
125 interfaces between chains.
- A–n · 3197 Ų buried · 49 hydrogen bonds · protein-nucleic
- A–E · 3193 Ų buried · 50 hydrogen bonds · protein-nucleic
- A–O · 2948 Ų buried · 48 hydrogen bonds · protein-nucleic
- A–L · 2840 Ų buried · 56 hydrogen bonds · protein-nucleic
- A–N · 2556 Ų buried · 62 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3JD5 · Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome · the same entry in another collection · chain N against N, 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 P82923
- Every structure of UniProt Q2M2T7
- Every structure of UniProt Q2KID9
- Every structure of UniProt P82931
- Every structure of UniProt Q3T040
- Every structure of UniProt Q58DQ5
- Every structure of UniProt P82670
- Every structure of UniProt P82911
- Every structure of UniProt Q29RU1
- Every structure of UniProt Q6B860
- Every structure of UniProt E1BBB4
- Every structure of UniProt P82915
- Every structure of UniProt P82916
- Every structure of UniProt P82917
- Every structure of UniProt P82920
- Every structure of UniProt P82649
- Every structure of UniProt Q2NL27
- Every structure of UniProt P82669
- Every structure of UniProt Q3SZ86
- Every structure of UniProt Q32PI8
- Every structure of UniProt P82928
- Every structure of UniProt P82922
- Every structure of UniProt P82925
- Every structure of UniProt P82926
- Every structure of UniProt P82929
- Every structure of UniProt Q2YDF6
- Every structure of UniProt Q2HJE8
- Every structure of UniProt Q0VCJ1
- Every structure of UniProt Q2KI62
- Every structure of UniProt P82918
- Elsewhere: RCSB PDB 3JD5 · PDBe 3JD5 · UniProt P82923 · UniProt Q2M2T7 · UniProt Q2KID9 · UniProt P82931 · UniProt Q3T040 · UniProt Q58DQ5 · UniProt P82670 · UniProt P82911 · UniProt Q29RU1 · UniProt Q6B860 · UniProt E1BBB4 · UniProt P82915 · UniProt P82916 · UniProt P82917 · UniProt P82920 · UniProt P82649 · UniProt Q2NL27 · UniProt P82669 · UniProt Q3SZ86 · UniProt Q32PI8 · UniProt P82928 · UniProt P82922 · UniProt P82925 · UniProt P82926 · UniProt P82929 · UniProt Q2YDF6 · UniProt Q2HJE8 · UniProt Q0VCJ1 · UniProt Q2KI62 · UniProt P82918
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