MolNFT v1 · #170558 · protein
Structure of a human 48S translational initiation complex - EIF3
6YBD · Eukaryotic translation initiation factor 3 subunit M: “Structure of a human 48S translational initiation complex - EIF3”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #170558 on GenesisL1: 3D structure…
- PDB
- 6YBD
- Type
- protein
- Length
- 4,421 residues
- Chains
- 19
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 3 subunit M; Eukaryotic translation initiation…
- EC
- 3.4.19.12
- UniProt
- Q7L2H7, O00303, Q14152, P60228, Q99613, O15372, P62081, P42677, P63220, P08708, P15880, P61247, P08865, P62854, P62263, P62277, O15371, Q9UBQ5, Q9Y262
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 19 distinct chains · 42% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 6 | Eukaryotic translation initiation factor 3 subunit M | protein | 350 | 37% helix, 0% strand | Q7L2H7 |
| 4 | Eukaryotic translation initiation factor 3 subunit F (EC 3.4.19.12) | protein | 257 | 45% helix, 11% strand | O00303 |
| u | Eukaryotic translation initiation factor 3 subunit a | protein | 572 | 59% helix, 2% strand | Q14152 |
| v | Eukaryotic translation initiation factor 3 subunit E | protein | 384 | 45% helix, 2% strand | P60228 |
| y | Eukaryotic translation initiation factor 3 subunit C | protein | 535 | 57% helix, 3% strand | Q99613 |
| 8 | Eukaryotic translation initiation factor 3 subunit H | protein | 317 | 42% helix, 12% strand | O15372 |
| G | 40S ribosomal protein S7 | protein | 177 | 24% helix, 18% strand | P62081 |
| H | 40S ribosomal protein S27 | protein | 81 | 4% helix, 22% strand | P42677 |
| K | 40S ribosomal protein S21 | protein | 81 | 19% helix, 10% strand | P63220 |
| M | 40S ribosomal protein S17 | protein | 54 | 17% helix, 11% strand | P08708 |
| L | 40S ribosomal protein S2 | protein | 220 | 26% helix, 22% strand | P15880 |
| O | 40S ribosomal protein S3A | protein | 211 | 22% helix, 30% strand | P61247 |
| N | 40S ribosomal protein sa | protein | 207 | 30% helix, 14% strand | P08865 |
| Q | 40S ribosomal protein S26 | protein | 99 | 8% helix, 24% strand | P62854 |
| P | 40S ribosomal protein S14 | protein | 133 | 21% helix, 25% strand | P62263 |
| I | 40S ribosomal protein S13 | protein | 150 | 34% helix, 0% strand | P62277 |
| x | Eukaryotic translation initiation factor 3 subunit D | protein | 61 | 0% helix, 2% strand | O15371 |
| 3 | Eukaryotic translation initiation factor 3 subunit K | protein | 213 | 65% helix, 2% strand | Q9UBQ5 |
| 5 | Eukaryotic translation initiation factor 3 subunit L | protein | 319 | 68% helix, 3% strand | Q9Y262 |
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 | 936 | 0.85 | 0.87 | 162 | empty |
| 2 | 1067 | 0.85 | 0.85 | 88 | empty |
| 3 | 1060 | 0.83 | 0.84 | 156 | empty |
| 4 | 1116 | 0.77 | 0.79 | 79 | empty |
| 5 | 1167 | 0.77 | 0.79 | 124 | empty |
Interfaces
37 interfaces between chains.
- u–y · 2767 Ų buried · 30 hydrogen bonds · protein-protein
- y–x · 2101 Ų buried · 16 hydrogen bonds · protein-protein
- K–N · 1527 Ų buried · 24 hydrogen bonds · protein-protein
- K–L · 1470 Ų buried · 15 hydrogen bonds · protein-protein
- M–N · 1382 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6YBD · Structure of a human 48S translational initiation complex - eIF3 · the same entry in another collection · chain u against u, 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 Q7L2H7
- Every structure of UniProt O00303
- Every structure of UniProt Q14152
- Every structure of UniProt P60228
- Every structure of UniProt Q99613
- Every structure of UniProt O15372
- Every structure of UniProt P62081
- Every structure of UniProt P42677
- Every structure of UniProt P63220
- 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 P62277
- Every structure of UniProt O15371
- Every structure of UniProt Q9UBQ5
- Every structure of UniProt Q9Y262
- Elsewhere: RCSB PDB 6YBD · PDBe 6YBD · UniProt Q7L2H7 · UniProt O00303 · UniProt Q14152 · UniProt P60228 · UniProt Q99613 · UniProt O15372 · UniProt P62081 · UniProt P42677 · UniProt P63220 · UniProt P08708 · UniProt P15880 · UniProt P61247 · UniProt P08865 · UniProt P62854 · UniProt P62263 · UniProt P62277 · UniProt O15371 · UniProt Q9UBQ5 · UniProt Q9Y262
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