MolNFT v1 · #172403 · protein + RNA
Structure of a crosslinked yeast ABCE1-bound 43S pre-initiation complex
7A1G · 18S ribosomal RNA: “Structure of a crosslinked yeast ABCE1-bound 43S pre-initiation complex”. Electron microscopy, 4 ligands (SF4, ADP, MG), 20 pockets (best druggability 0.88). MolNFT v1 #172403 on GenesisL1: 3D structure, binding…
- PDB
- 7A1G
- Type
- protein + RNA
- Length
- 7,383 residues
- Chains
- 37
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 18S ribosomal RNA; 40S ribosomal protein S0-a; 40S ribosomal protein S1-a; 40S ribosomal…
- UniProt
- P32905, P33442, P25443, P0CX35, P0CX37, P26786, P0CX39, O13516, P0CX47, P05756, P39516, P0C0V8, P0C0W1, P0CX29, P0CX31, P39939, P35997, P0CX33, Q01855, P05750, P26783, Q08745, P48589, P0CX51, P14127, P0CX55, P07280, P38701, Q3E792, P41057, P05759, P38011, Q3E7X9, Q05775, Q03195
- Ligands
- SF4, ADP, MG, ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 37 distinct chains · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 2 | 18S ribosomal RNA | rna | 1771 | — | — |
| P | 40S ribosomal protein S0-a | protein | 206 | 34% helix, 15% strand | P32905 |
| Q | 40S ribosomal protein S1-a | protein | 226 | 26% helix, 28% strand | P33442 |
| R | 40S ribosomal protein S2 | protein | 216 | 33% helix, 28% strand | P25443 |
| S | 40S ribosomal protein S4-a | protein | 258 | 15% helix, 29% strand | P0CX35 |
| T | 40S ribosomal protein S6-a | protein | 228 | 29% helix, 23% strand | P0CX37 |
| U | 40S ribosomal protein S7-a | protein | 184 | 36% helix, 21% strand | P26786 |
| V | 40S ribosomal protein S8-a | protein | 187 | 27% helix, 27% strand | P0CX39 |
| W | 40S ribosomal protein S9-a | protein | 184 | 49% helix, 2% strand | O13516 |
| X | 40S ribosomal protein S11-a | protein | 142 | 4% helix, 31% strand | P0CX47 |
| Y | 40S ribosomal protein S13 | protein | 150 | 55% helix, 0% strand | P05756 |
| Z | 40S ribosomal protein S14-B | protein | 127 | 27% helix, 27% strand | P39516 |
| a | 40S ribosomal protein S21-a | protein | 87 | 18% helix, 30% strand | P0C0V8 |
| b | 40S ribosomal protein S22-a | protein | 129 | 35% helix, 27% strand | P0C0W1 |
| c | 40S ribosomal protein S23-a | protein | 144 | 22% helix, 26% strand | P0CX29 |
| d | 40S ribosomal protein S24-a | protein | 134 | 36% helix, 25% strand | P0CX31 |
| e | 40S ribosomal protein S26-B | protein | 97 | 16% helix, 21% strand | P39939 |
| f | 40S ribosomal protein S27-a | protein | 81 | 7% helix, 21% strand | P35997 |
| g | 40S ribosomal protein S30-a | protein | 60 | 35% helix, 0% strand | P0CX33 |
| E | 40S ribosomal protein S15 | protein | 117 | 29% helix, 15% strand | Q01855 |
| A | 40S ribosomal protein S3 | protein | 222 | 39% helix, 29% strand | P05750 |
| B | 40S ribosomal protein S5 | protein | 206 | 45% helix, 6% strand | P26783 |
| C | 40S ribosomal protein S10-a | protein | 92 | 40% helix, 10% strand | Q08745 |
| D | 40S ribosomal protein S12 | protein | 121 | 36% helix, 10% strand | P48589 |
| F | 40S ribosomal protein S16-a | protein | 141 | 43% helix, 20% strand | P0CX51 |
| H | 40S ribosomal protein S17-B | protein | 121 | 52% helix, 5% strand | P14127 |
| I | 40S ribosomal protein S18-a | protein | 145 | 37% helix, 8% strand | P0CX55 |
| J | 40S ribosomal protein S19-a | protein | 143 | 44% helix, 10% strand | P07280 |
| K | 40S ribosomal protein S20 | protein | 100 | 26% helix, 37% strand | P38701 |
| L | 40S ribosomal protein S25-a | protein | 82 | 39% helix, 21% strand | Q3E792 |
| M | 40S ribosomal protein S29-a | protein | 53 | 26% helix, 9% strand | P41057 |
| N | Ubiquitin-40S ribosomal protein S31 | protein | 73 | 0% helix, 3% strand | P05759 |
| O | Guanine nucleotide-binding protein subunit beta-like protein | protein | 312 | 0% helix, 53% strand | P38011 |
| h | 40S ribosomal protein S28-a | protein | 63 | 0% helix, 48% strand | Q3E7X9 |
| z | Eukaryotic translation initiation factor 3 subunit J | protein | 120 | 57% helix, 2% strand | Q05775 |
| y | Eukaryotic translation initiation factor 3 subunit J | protein | 79 | 80% helix, 0% strand | Q05775 |
| x | Translation initiation factor RLI1 | protein | 582 | 31% helix, 15% strand | Q03195 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains x
- ADP · Adenosine-5'-diphosphate · ligand · chains x
- MG · Magnesium ion · metal · 80 copies · chains 2, e, Y, J, c, K, R, S, B, x
- ZN · Zinc ion · metal · 2 copies · chains M, 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 | 755 | 0.88 | 0.93 | 86 | MG |
| 2 | 910 | 0.88 | 0.91 | 86 | MG |
| 3 | 620 | 0.88 | 0.93 | 75 | empty |
| 4 | 652 | 0.87 | 0.92 | 79 | MG |
| 5 | 689 | 0.85 | 0.90 | 57 | empty |
Interfaces
100 interfaces between chains.
- 2–T · 5220 Ų buried · 110 hydrogen bonds · protein-nucleic
- 2–S · 4020 Ų buried · 68 hydrogen bonds · protein-nucleic
- 2–V · 3855 Ų buried · 100 hydrogen bonds · protein-nucleic
- 2–c · 3705 Ų buried · 75 hydrogen bonds · protein-nucleic
- 2–W · 3498 Ų buried · 72 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7A1G · Structure of a crosslinked yeast ABCE1-bound 43S pre-initiation complex · the same entry in another collection · chain X against X, 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 P32905
- Every structure of UniProt P33442
- Every structure of UniProt P25443
- Every structure of UniProt P0CX35
- Every structure of UniProt P0CX37
- Every structure of UniProt P26786
- Every structure of UniProt P0CX39
- Every structure of UniProt O13516
- Every structure of UniProt P0CX47
- Every structure of UniProt P05756
- Every structure of UniProt P39516
- Every structure of UniProt P0C0V8
- Every structure of UniProt P0C0W1
- Every structure of UniProt P0CX29
- Every structure of UniProt P0CX31
- Every structure of UniProt P39939
- Every structure of UniProt P35997
- Every structure of UniProt P0CX33
- Every structure of UniProt Q01855
- Every structure of UniProt P05750
- Every structure of UniProt P26783
- Every structure of UniProt Q08745
- Every structure of UniProt P48589
- Every structure of UniProt P0CX51
- Every structure of UniProt P14127
- Every structure of UniProt P0CX55
- Every structure of UniProt P07280
- Every structure of UniProt P38701
- Every structure of UniProt Q3E792
- Every structure of UniProt P41057
- Every structure of UniProt P05759
- Every structure of UniProt P38011
- Every structure of UniProt Q3E7X9
- Every structure of UniProt Q05775
- Every structure of UniProt Q03195
- Elsewhere: RCSB PDB 7A1G · PDBe 7A1G · UniProt P32905 · UniProt P33442 · UniProt P25443 · UniProt P0CX35 · UniProt P0CX37 · UniProt P26786 · UniProt P0CX39 · UniProt O13516 · UniProt P0CX47 · UniProt P05756 · UniProt P39516 · UniProt P0C0V8 · UniProt P0C0W1 · UniProt P0CX29 · UniProt P0CX31 · UniProt P39939 · UniProt P35997 · UniProt P0CX33 · UniProt Q01855 · UniProt P05750 · UniProt P26783 · UniProt Q08745 · UniProt P48589 · UniProt P0CX51 · UniProt P14127 · UniProt P0CX55 · UniProt P07280 · UniProt P38701 · UniProt Q3E792 · UniProt P41057 · UniProt P05759 · UniProt P38011 · UniProt Q3E7X9 · UniProt Q05775 · UniProt Q03195
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