Research workbench
Human mitochondrial small subunit assembly intermediate (State E)
Analyse Human mitochondrial small subunit assembly intermediate (State E) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8CST
- Type
- protein + RNA
- Length
- 6,698 residues
- Chains
- 32
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.85
- Source
- Homo sapiens
- Molecule
- 28S ribosomal protein S34, mitochondrial; 28S ribosomal protein S35, mitochondrial…
- EC
- 2.1.1.-
- UniProt
- P82930, P82673, Q9NWT8, Q96EY7, Q8N0V3, Q9H7H0, Q9Y399, Q96EL2, P82675, P82932, Q9Y2R9, P82933, P82664, P82912, O15235, O60783, P82914, Q9Y3D3, Q9Y2R5, Q9Y676, Q9Y3D5, P82921, P82650, Q9Y3D9, P82663, Q9BYN8, Q92552, Q9Y2Q9, P51398, Q92665, Q9Y291
- Ligands
- FES, SF4, SAM, NAD, ATP, GDP, MG, K, ZN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · resolution 2.85 · 32 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | 28S ribosomal protein S34, mitochondrial | protein | 211 | 31% helix, 18% strand | P82930 |
| 1 | 28S ribosomal protein S35, mitochondrial | protein | 259 | 49% helix, 10% strand | P82673 |
| 3 | Aurora kinase A-interacting protein | protein | 70 | 71% helix, 0% strand | Q9NWT8 |
| 4 | Pentatricopeptide repeat domain-containing protein 3, mitochondrial | protein | 566 | 68% helix, 1% strand | Q96EY7 |
| 6 | Putative ribosome-binding factor A, mitochondrial | protein | 126 | 52% helix, 14% strand | Q8N0V3 |
| 7 | Methyltransferase-like protein 17, mitochondrial (EC 2.1.1.-) | protein | 400 | 37% helix, 19% strand | Q9H7H0 |
| A | 12S mitochondrial rRNA | rna | 888 | — | — |
| B | 28S ribosomal protein S2, mitochondrial | protein | 220 | 49% helix, 16% strand | Q9Y399 |
| C | 28S ribosomal protein S24, mitochondrial | protein | 126 | 38% helix, 21% strand | Q96EL2 |
| D | 28S ribosomal protein S5, mitochondrial | protein | 232 | 24% helix, 27% strand | P82675 |
| E | 28S ribosomal protein S6, mitochondrial | protein | 108 | 31% helix, 46% strand | P82932 |
| F | 28S ribosomal protein S7, mitochondrial | protein | 206 | 54% helix, 8% strand | Q9Y2R9 |
| G | 28S ribosomal protein S9, mitochondrial | protein | 292 | 46% helix, 14% strand | P82933 |
| H | 28S ribosomal protein S10, mitochondrial | protein | 130 | 26% helix, 44% strand | P82664 |
| I | 28S ribosomal protein S11, mitochondrial | protein | 137 | 26% helix, 26% strand | P82912 |
| J | 28S ribosomal protein S12, mitochondrial | protein | 107 | 7% helix, 33% strand | O15235 |
| K | 28S ribosomal protein S14, mitochondrial | protein | 100 | 55% helix, 7% strand | O60783 |
| L | 28S ribosomal protein S15, mitochondrial | protein | 161 | 66% helix, 1% strand | P82914 |
| M | 28S ribosomal protein S16, mitochondrial | protein | 115 | 37% helix, 30% strand | Q9Y3D3 |
| N | 28S ribosomal protein S17, mitochondrial | protein | 109 | 3% helix, 50% strand | Q9Y2R5 |
| O | 28S ribosomal protein S18b, mitochondrial | protein | 190 | 31% helix, 3% strand | Q9Y676 |
| P | 28S ribosomal protein S18c, mitochondrial | protein | 96 | 32% helix, 2% strand | Q9Y3D5 |
| Q | 28S ribosomal protein S21, mitochondrial | protein | 86 | 57% helix, 5% strand | P82921 |
| R | 28S ribosomal protein S22, mitochondrial | protein | 291 | 55% helix, 8% strand | P82650 |
| S | 28S ribosomal protein S23, mitochondrial | protein | 133 | 43% helix, 2% strand | Q9Y3D9 |
| T | 28S ribosomal protein S25, mitochondrial | protein | 164 | 39% helix, 18% strand | P82663 |
| U | 28S ribosomal protein S26, mitochondrial | protein | 174 | 69% helix, 3% strand | Q9BYN8 |
| V | 28S ribosomal protein S27, mitochondrial | protein | 359 | 72% helix, 1% strand | Q92552 |
| W | 28S ribosomal protein S28, mitochondrial | protein | 98 | 14% helix, 41% strand | Q9Y2Q9 |
| X | 28S ribosomal protein S29, mitochondrial | protein | 352 | 46% helix, 15% strand | P51398 |
| Y | 28S ribosomal protein S31, mitochondrial | protein | 123 | 51% helix, 0% strand | Q92665 |
| Z | 28S ribosomal protein S33, mitochondrial | protein | 69 | 49% helix, 0% strand | Q9Y291 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, P, M, T
- SF4 · Iron/sulfur cluster · ligand · chains 7
- SAM · S-adenosylmethionine · ligand · chains 7
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A, J, L
- ATP · Adenosine-5'-triphosphate · ligand · chains X
- GDP · Guanosine-5'-diphosphate · ligand · chains X
- MG · Magnesium ion · metal · 30 copies · chains A, D, M, 7, B, W, X
- K · Potassium ion · metal · 4 copies · chains A
- ZN · Zinc ion · metal · chains O
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 | 782 | 0.85 | 0.88 | 62 | MG |
| 2 | 1173 | 0.84 | 0.86 | 71 | empty |
| 3 | 907 | 0.84 | 0.86 | 67 | empty |
| 4 | 1153 | 0.83 | 0.84 | 104 | empty |
| 5 | 685 | 0.83 | 0.87 | 79 | ATP, MG |
Interfaces
103 interfaces between chains.
- A–L · 2694 Ų buried · 59 hydrogen bonds · protein-nucleic
- 4–Y · 2539 Ų buried · 16 hydrogen bonds · protein-protein
- A–J · 2478 Ų buried · 58 hydrogen bonds · protein-nucleic
- 1–H · 2337 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 2310 Ų buried · 37 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 modified (nucleotide modification, nonstandard).
Compared structures
- P51398 · AlphaFold monomer V2.0 prediction for 28S ribosomal protein S29, mitochondrial (P51398) · a predicted model of the same protein · chain X against A, TM-score 0.99
- Q92552 · AlphaFold monomer V2.0 prediction for 28S ribosomal protein S27, mitochondrial (Q92552) · a predicted model of the same protein · chain V against A, TM-score 0.99
- Q96EY7 · AlphaFold monomer V2.0 prediction for pentatricopeptide repeat domain-containing protein… · a predicted model of the same protein · chain 4 against A, TM-score 0.99
- P82650 · AlphaFold monomer V2.0 prediction for 28S ribosomal protein S22, mitochondrial (P82650) · a predicted model of the same protein · chain R against A, TM-score 0.99
- Q9Y399 · AlphaFold monomer V2.0 prediction for 28S ribosomal protein S2, mitochondrial (Q9Y399) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P82912 · AlphaFold monomer V2.0 prediction for 28S ribosomal protein S11, mitochondrial (P82912) · a predicted model of the same protein · chain I against A, TM-score 0.99
- P82675 · AlphaFold monomer V2.0 prediction for 28S ribosomal protein S5, mitochondrial (P82675) · a predicted model of the same protein · chain D against A, TM-score 0.99
- P82932 · AlphaFold monomer V2.0 prediction for 28S ribosomal protein S6, mitochondrial (P82932) · a predicted model of the same protein · chain E against A, TM-score 0.99
- Q9Y2Q9 · AlphaFold monomer V2.0 prediction for 28S ribosomal protein S28, mitochondrial (Q9Y2Q9) · a predicted model of the same protein · chain W against A, TM-score 0.98
- Q9Y2R9 · AlphaFold monomer V2.0 prediction for 28S ribosomal protein S7, mitochondrial (Q9Y2R9) · a predicted model of the same protein · chain F against A, TM-score 0.98
- O60783 · AlphaFold monomer V2.0 prediction for 28S ribosomal protein S14, mitochondrial (O60783) · a predicted model of the same protein · chain K against A, TM-score 0.98
- P82914 · AlphaFold monomer V2.0 prediction for 28S ribosomal protein S15, mitochondrial (P82914) · a predicted model of the same protein · chain L against A, TM-score 0.97
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 P82930
- Every structure of UniProt P82673
- Every structure of UniProt Q9NWT8
- Every structure of UniProt Q96EY7
- Every structure of UniProt Q8N0V3
- Every structure of UniProt Q9H7H0
- Every structure of UniProt Q9Y399
- Every structure of UniProt Q96EL2
- Every structure of UniProt P82675
- Every structure of UniProt P82932
- Every structure of UniProt Q9Y2R9
- Every structure of UniProt P82933
- Every structure of UniProt P82664
- Every structure of UniProt P82912
- Every structure of UniProt O15235
- Every structure of UniProt O60783
- Every structure of UniProt P82914
- Every structure of UniProt Q9Y3D3
- Every structure of UniProt Q9Y2R5
- Every structure of UniProt Q9Y676
- Every structure of UniProt Q9Y3D5
- Every structure of UniProt P82921
- Every structure of UniProt P82650
- Every structure of UniProt Q9Y3D9
- Every structure of UniProt P82663
- Every structure of UniProt Q9BYN8
- Every structure of UniProt Q92552
- Every structure of UniProt Q9Y2Q9
- Every structure of UniProt P51398
- Every structure of UniProt Q92665
- Every structure of UniProt Q9Y291
- Elsewhere: RCSB PDB 8CST · PDBe 8CST · UniProt P82930 · UniProt P82673 · UniProt Q9NWT8 · UniProt Q96EY7 · UniProt Q8N0V3 · UniProt Q9H7H0 · UniProt Q9Y399 · UniProt Q96EL2 · UniProt P82675 · UniProt P82932 · UniProt Q9Y2R9 · UniProt P82933 · UniProt P82664 · UniProt P82912 · UniProt O15235 · UniProt O60783 · UniProt P82914 · UniProt Q9Y3D3 · UniProt Q9Y2R5 · UniProt Q9Y676 · UniProt Q9Y3D5 · UniProt P82921 · UniProt P82650 · UniProt Q9Y3D9 · UniProt P82663 · UniProt Q9BYN8 · UniProt Q92552 · UniProt Q9Y2Q9 · UniProt P51398 · UniProt Q92665 · UniProt Q9Y291
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