MolNFT v1 · #170576 · protein + RNA
Structure of a human 48S translational initiation complex - 40S body
6YBW · 40S ribosomal protein S4, X isoform: “Structure of a human 48S translational initiation complex - 40S body”. Electron microscopy, 2 ligands (MG, ZN), 20 pockets (best druggability 0.87). MolNFT v1 #170576 on GenesisL1: 3D structure…
- PDB
- 6YBW
- Type
- protein + RNA
- Length
- 4,622 residues
- Chains
- 26
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 40S ribosomal protein S4, X isoform; 40S ribosomal protein S11; 40S ribosomal protein…
- UniProt
- P62701, P62280, P62266, P46781, P62081, P62861, P42677, P63220, P62244, P08708, P15880, P61247, P08865, P62854, P62263, P62753, P62241, P62847, P47813, P41567, P62277, O75822, Q99613, P62945
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 26 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 40S ribosomal protein S4, X isoform | protein | 256 | 13% helix, 32% strand | P62701 |
| B | 40S ribosomal protein S11 | protein | 142 | 0% helix, 32% strand | P62280 |
| E | 40S ribosomal protein S23 | protein | 140 | 19% helix, 29% strand | P62266 |
| D | 40S ribosomal protein S9 | protein | 177 | 45% helix, 6% strand | P46781 |
| G | 40S ribosomal protein S7 | protein | 177 | 36% helix, 23% strand | P62081 |
| F | 40S ribosomal protein S30 | protein | 47 | 36% helix, 0% strand | P62861 |
| H | 40S ribosomal protein S27 | protein | 81 | 7% helix, 26% strand | P42677 |
| K | 40S ribosomal protein S21 | protein | 81 | 20% helix, 27% strand | P63220 |
| J | 40S ribosomal protein S15A | protein | 129 | 30% helix, 29% strand | P62244 |
| M | 40S ribosomal protein S17 | protein | 54 | 17% helix, 11% strand | P08708 |
| L | 40S ribosomal protein S2 | protein | 220 | 30% helix, 24% strand | P15880 |
| O | 40S ribosomal protein S3A | protein | 211 | 29% helix, 34% strand | P61247 |
| N | 40S ribosomal protein sa | protein | 207 | 36% helix, 14% strand | P08865 |
| Q | 40S ribosomal protein S26 | protein | 99 | 19% helix, 20% strand | P62854 |
| P | 40S ribosomal protein S14 | protein | 131 | 24% helix, 26% strand | P62263 |
| S | 40S ribosomal protein S6 | protein | 230 | 27% helix, 22% strand | P62753 |
| R | 40S ribosomal protein S8 | protein | 198 | 23% helix, 25% strand | P62241 |
| T | 40S ribosomal protein S24 | protein | 125 | 35% helix, 26% strand | P62847 |
| q | Eukaryotic translation initiation factor 1A, X-chromosomal | protein | 88 | 6% helix, 24% strand | P47813 |
| p | Eukaryotic translation initiation factor 1 | protein | 85 | 24% helix, 31% strand | P41567 |
| I | 40S ribosomal protein S13 | protein | 150 | 55% helix, 0% strand | P62277 |
| z | Eukaryotic translation initiation factor 3 subunit J | protein | 160 | 63% helix, 0% strand | O75822 |
| y | Eukaryotic translation initiation factor 3 subunit C | protein | 162 | 69% helix, 0% strand | Q99613 |
| 9 | 60S ribosomal protein L41 | protein | 24 | 83% helix, 0% strand | P62945 |
| A | 18S rRNA | rna | 1220 | — | — |
| 7 | MRNA | rna | 28 | — | — |
Ligands and binding sites
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 | 772 | 0.87 | 0.91 | 82 | MG |
| 2 | 1188 | 0.86 | 0.88 | 79 | empty |
| 3 | 684 | 0.86 | 0.91 | 56 | MG |
| 4 | 1053 | 0.86 | 0.88 | 86 | MG |
| 5 | 784 | 0.86 | 0.89 | 71 | empty |
Interfaces
67 interfaces between chains.
- S–A · 5444 Ų buried · 126 hydrogen bonds · protein-nucleic
- R–A · 4264 Ų buried · 112 hydrogen bonds · protein-nucleic
- C–A · 3928 Ų buried · 64 hydrogen bonds · protein-nucleic
- E–A · 3669 Ų buried · 73 hydrogen bonds · protein-nucleic
- D–A · 3643 Ų buried · 77 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 24 modified (nucleotide modification).
Compared structures
- 6YBW · Structure of a human 48S translational initiation complex - 40S body · the same entry in another collection · chain L against L, 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 P62701
- Every structure of UniProt P62280
- Every structure of UniProt P62266
- Every structure of UniProt P46781
- Every structure of UniProt P62081
- Every structure of UniProt P62861
- Every structure of UniProt P42677
- Every structure of UniProt P63220
- Every structure of UniProt P62244
- Every structure of UniProt P08708
- Every structure of UniProt P15880
- Every structure of UniProt P61247
- Every structure of UniProt P08865
- Every structure of UniProt P62854
- Every structure of UniProt P62263
- Every structure of UniProt P62753
- Every structure of UniProt P62241
- Every structure of UniProt P62847
- Every structure of UniProt P47813
- Every structure of UniProt P41567
- Every structure of UniProt P62277
- Every structure of UniProt O75822
- Every structure of UniProt Q99613
- Every structure of UniProt P62945
- Elsewhere: RCSB PDB 6YBW · PDBe 6YBW · UniProt P62701 · UniProt P62280 · UniProt P62266 · UniProt P46781 · UniProt P62081 · UniProt P62861 · UniProt P42677 · UniProt P63220 · UniProt P62244 · UniProt P08708 · UniProt P15880 · UniProt P61247 · UniProt P08865 · UniProt P62854 · UniProt P62263 · UniProt P62753 · UniProt P62241 · UniProt P62847 · UniProt P47813 · UniProt P41567 · UniProt P62277 · UniProt O75822 · UniProt Q99613 · UniProt P62945
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