Research workbench
Structure of a yeast ABCE1-bound 43S pre-initiation complex
Analyse Structure of a yeast ABCE1-bound 43S pre-initiation complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZCE
- Type
- protein + RNA
- Length
- 9,746 residues
- Chains
- 45
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 3 subunit I; Eukaryotic translation initiation…
- UniProt
- P40217, Q04067, P32905, P33442, P25443, P05750, P0CX35, P26783, P0CX37, P26786, P0CX39, O13516, Q08745, P0CX47, P48589, P05756, P06367, Q01855, P0CX51, P02407, P0CX55, P07280, P38701, P0C0V8, P0C0W1, P0CX29, P0CX31, Q3E792, P39938, P35997, P0C0X0, P41057, P0CX33, P05759, P38011, P38249, P06103, P32497, P38912, P32911, Q05775, Q03195
- Ligands
- SF4, ADP, ATP, ZN, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 45 distinct chains · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| l | Eukaryotic translation initiation factor 3 subunit I | protein | 330 | 6% helix, 52% strand | P40217 |
| r | Eukaryotic translation initiation factor 3 subunit G | protein | 53 | 36% helix, 6% strand | Q04067 |
| A | 18S ribosomal RNA (1719-mer) | rna | 1719 | — | — |
| B | 40S ribosomal protein S0-a | protein | 206 | 31% helix, 15% strand | P32905 |
| C | 40S ribosomal protein S1-a | protein | 214 | 29% helix, 29% strand | P33442 |
| D | 40S ribosomal protein S2 | protein | 217 | 30% helix, 27% strand | P25443 |
| E | 40S ribosomal protein S3 | protein | 223 | 36% helix, 26% strand | P05750 |
| F | 40S ribosomal protein S4-a | protein | 260 | 14% helix, 27% strand | P0CX35 |
| G | 40S ribosomal protein S5 | protein | 206 | 50% helix, 4% strand | P26783 |
| H | 40S ribosomal protein S6-a | protein | 226 | 30% helix, 24% strand | P0CX37 |
| I | 40S ribosomal protein S7-a | protein | 184 | 33% helix, 18% strand | P26786 |
| J | 40S ribosomal protein S8-a | protein | 188 | 26% helix, 27% strand | P0CX39 |
| K | 40S ribosomal protein S9-a | protein | 184 | 47% helix, 2% strand | O13516 |
| L | 40S ribosomal protein S10-a | protein | 92 | 40% helix, 12% strand | Q08745 |
| M | 40S ribosomal protein S11-a | protein | 142 | 3% helix, 32% strand | P0CX47 |
| N | 40S ribosomal protein S12 | protein | 120 | 39% helix, 5% strand | P48589 |
| O | 40S ribosomal protein S13 | protein | 150 | 55% helix, 0% strand | P05756 |
| P | 40S ribosomal protein S14-a | protein | 127 | 24% helix, 21% strand | P06367 |
| Q | 40S ribosomal protein S15 | protein | 122 | 32% helix, 11% strand | Q01855 |
| R | 40S ribosomal protein S16-a | protein | 141 | 34% helix, 20% strand | P0CX51 |
| S | 40S ribosomal protein S17-a | protein | 117 | 50% helix, 6% strand | P02407 |
| T | 40S ribosomal protein S18-a | protein | 145 | 32% helix, 6% strand | P0CX55 |
| U | 40S ribosomal protein S19-a | protein | 143 | 49% helix, 10% strand | P07280 |
| V | 40S ribosomal protein S20 | protein | 105 | 24% helix, 45% strand | P38701 |
| W | 40S ribosomal protein S21-a | protein | 87 | 17% helix, 18% strand | P0C0V8 |
| X | 40S ribosomal protein S22-a | protein | 129 | 33% helix, 26% strand | P0C0W1 |
| Y | 40S ribosomal protein S23-a | protein | 144 | 23% helix, 24% strand | P0CX29 |
| Z | 40S ribosomal protein S24-a | protein | 134 | 33% helix, 26% strand | P0CX31 |
| a | 40S ribosomal protein S25-a | protein | 70 | 36% helix, 6% strand | Q3E792 |
| b | 40S ribosomal protein S26-a | protein | 97 | 10% helix, 20% strand | P39938 |
| c | 40S ribosomal protein S27-a | protein | 81 | 7% helix, 26% strand | P35997 |
| d | 40S ribosomal protein S28-B | protein | 62 | 0% helix, 48% strand | P0C0X0 |
| e | 40S ribosomal protein S29-a | protein | 53 | 25% helix, 9% strand | P41057 |
| f | 40S ribosomal protein S30-a | protein | 53 | 34% helix, 0% strand | P0CX33 |
| g | Ubiquitin-40S ribosomal protein S31 | protein | 71 | 0% helix, 21% strand | P05759 |
| h | Guanine nucleotide-binding protein subunit beta-like protein | protein | 318 | 0% helix, 53% strand | P38011 |
| o | Eukaryotic translation initiation factor 3 subunit a | protein | 529 | 70% helix, 2% strand | P38249 |
| p | Eukaryotic translation initiation factor 3 subunit B | protein | 646 | 13% helix, 37% strand | P06103 |
| q | Eukaryotic translation initiation factor 3 subunit C | protein | 636 | 64% helix, 0% strand | P32497 |
| i | Eukaryotic translation initiation factor 1A | protein | 97 | 10% helix, 30% strand | P38912 |
| m | Eukaryotic translation initiation factor eif-1 | protein | 90 | 16% helix, 18% strand | P32911 |
| t | Eukaryotic translation initiation factor 3 subunit J | protein | 84 | 73% helix, 0% strand | Q05775 |
| j | RNA recognition motif (unknown) | protein | 77 | 21% helix, 31% strand | — |
| k | Translation initiation factor RLI1 | protein | 579 | 30% helix, 18% strand | Q03195 |
| s | Eukaryotic translation initiation factor 3 subunit J | protein | 95 | 68% helix, 0% strand | Q05775 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains k
- ADP · Adenosine-5'-diphosphate · ligand · chains k
- ATP · Adenosine-5'-triphosphate · ligand · chains k
- ZN · Zinc ion · metal · 4 copies · chains A, e, b, c, g
- MG · Magnesium ion · metal · 2 copies · chains k
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 | 1077 | 0.88 | 0.90 | 101 | empty |
| 2 | 890 | 0.86 | 0.89 | 131 | empty |
| 3 | 1154 | 0.86 | 0.87 | 179 | empty |
| 4 | 810 | 0.86 | 0.89 | 101 | empty |
| 5 | 652 | 0.86 | 0.91 | 64 | empty |
Interfaces
105 interfaces between chains.
- A–H · 2404 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–J · 2287 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–F · 2024 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–Y · 1957 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–K · 1793 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6ZCE · Structure of a yeast ABCE1-bound 43S pre-initiation complex · the same entry in another collection · chain A against A, 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 P40217
- Every structure of UniProt Q04067
- Every structure of UniProt P32905
- Every structure of UniProt P33442
- Every structure of UniProt P25443
- Every structure of UniProt P05750
- Every structure of UniProt P0CX35
- Every structure of UniProt P26783
- Every structure of UniProt P0CX37
- Every structure of UniProt P26786
- Every structure of UniProt P0CX39
- Every structure of UniProt O13516
- Every structure of UniProt Q08745
- Every structure of UniProt P0CX47
- Every structure of UniProt P48589
- Every structure of UniProt P05756
- Every structure of UniProt P06367
- Every structure of UniProt Q01855
- Every structure of UniProt P0CX51
- Every structure of UniProt P02407
- Every structure of UniProt P0CX55
- Every structure of UniProt P07280
- Every structure of UniProt P38701
- Every structure of UniProt P0C0V8
- Every structure of UniProt P0C0W1
- Every structure of UniProt P0CX29
- Every structure of UniProt P0CX31
- Every structure of UniProt Q3E792
- Every structure of UniProt P39938
- Every structure of UniProt P35997
- Every structure of UniProt P0C0X0
- Every structure of UniProt P41057
- Every structure of UniProt P0CX33
- Every structure of UniProt P05759
- Every structure of UniProt P38011
- Every structure of UniProt P38249
- Every structure of UniProt P06103
- Every structure of UniProt P32497
- Every structure of UniProt P38912
- Every structure of UniProt P32911
- Every structure of UniProt Q05775
- Every structure of UniProt Q03195
- Elsewhere: RCSB PDB 6ZCE · PDBe 6ZCE · UniProt P40217 · UniProt Q04067 · UniProt P32905 · UniProt P33442 · UniProt P25443 · UniProt P05750 · UniProt P0CX35 · UniProt P26783 · UniProt P0CX37 · UniProt P26786 · UniProt P0CX39 · UniProt O13516 · UniProt Q08745 · UniProt P0CX47 · UniProt P48589 · UniProt P05756 · UniProt P06367 · UniProt Q01855 · UniProt P0CX51 · UniProt P02407 · UniProt P0CX55 · UniProt P07280 · UniProt P38701 · UniProt P0C0V8 · UniProt P0C0W1 · UniProt P0CX29 · UniProt P0CX31 · UniProt Q3E792 · UniProt P39938 · UniProt P35997 · UniProt P0C0X0 · UniProt P41057 · UniProt P0CX33 · UniProt P05759 · UniProt P38011 · UniProt P38249 · UniProt P06103 · UniProt P32497 · UniProt P38912 · UniProt P32911 · UniProt Q05775 · UniProt Q03195
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