MolNFT v1 · #170572 · protein + RNA
Structure of a human 48S translational initiation complex - head
6YBS · Eukaryotic translation initiation factor 3 subunit D: “Structure of a human 48S translational initiation complex - head”. Electron microscopy, 2 ligands (MG, ZN), 20 pockets (best druggability 0.89). MolNFT v1 #170572 on GenesisL1…
- PDB
- 6YBS
- Type
- protein + RNA
- Length
- 2,831 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 3 subunit D; Receptor of activated protein C…
- EC
- 4.2.99.18
- UniProt
- O15371, P63244, P62857, P08708, P60866, O75821, P46783, P25398, P62273, P62841, P23396, P39019, P62851, P62269, P46782, P62979, P62249
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 18 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| x | Eukaryotic translation initiation factor 3 subunit D | protein | 360 | 21% helix, 20% strand | O15371 |
| c | Receptor of activated protein C kinase 1 | protein | 313 | 0% helix, 50% strand | P63244 |
| n | 40S ribosomal protein S28 | protein | 63 | 0% helix, 44% strand | P62857 |
| X | 40S ribosomal protein S17 | protein | 78 | 62% helix, 3% strand | P08708 |
| h | 40S ribosomal protein S20 | protein | 103 | 23% helix, 41% strand | P60866 |
| o | Eukaryotic translation initiation factor 3 subunit G | protein | 77 | 21% helix, 40% strand | O75821 |
| a | 40S ribosomal protein S10 | protein | 99 | 39% helix, 16% strand | P46783 |
| m | 40S ribosomal protein S12 | protein | 122 | 45% helix, 13% strand | P25398 |
| i | 40S ribosomal protein S29 | protein | 50 | 28% helix, 10% strand | P62273 |
| b | 40S ribosomal protein S15 | protein | 110 | 35% helix, 15% strand | P62841 |
| Z | 40S ribosomal protein S3 (EC 4.2.99.18) | protein | 227 | 33% helix, 26% strand | P23396 |
| d | 40S ribosomal protein S19 | protein | 142 | 51% helix, 14% strand | P39019 |
| e | 40S ribosomal protein S25 | protein | 66 | 47% helix, 15% strand | P62851 |
| f | 40S ribosomal protein S18 | protein | 142 | 43% helix, 6% strand | P62269 |
| V | 40S ribosomal protein S5 | protein | 184 | 48% helix, 6% strand | P46782 |
| k | Ubiquitin-40S ribosomal protein S27A | protein | 53 | 0% helix, 25% strand | P62979 |
| Y | 40S ribosomal protein S16 | protein | 141 | 40% helix, 22% strand | P62249 |
| A | 18S rRNA | rna | 501 | — | — |
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 | 1095 | 0.89 | 0.92 | 117 | MG |
| 2 | 743 | 0.87 | 0.90 | 74 | empty |
| 3 | 516 | 0.86 | 0.94 | 67 | empty |
| 4 | 682 | 0.85 | 0.90 | 67 | empty |
| 5 | 883 | 0.85 | 0.87 | 120 | empty |
Interfaces
40 interfaces between chains.
- Y–A · 3098 Ų buried · 61 hydrogen bonds · protein-nucleic
- d–A · 3069 Ų buried · 71 hydrogen bonds · protein-nucleic
- f–A · 2410 Ų buried · 66 hydrogen bonds · protein-nucleic
- i–A · 1990 Ų buried · 44 hydrogen bonds · protein-nucleic
- h–A · 1939 Ų buried · 30 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 6YBS · Structure of a human 48S translational initiation complex - head · the same entry in another collection · chain Z against Z, 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 O15371
- Every structure of UniProt P63244
- Every structure of UniProt P62857
- Every structure of UniProt P08708
- Every structure of UniProt P60866
- Every structure of UniProt O75821
- Every structure of UniProt P46783
- Every structure of UniProt P25398
- Every structure of UniProt P62273
- Every structure of UniProt P62841
- Every structure of UniProt P23396
- Every structure of UniProt P39019
- Every structure of UniProt P62851
- Every structure of UniProt P62269
- Every structure of UniProt P46782
- Every structure of UniProt P62979
- Every structure of UniProt P62249
- Elsewhere: RCSB PDB 6YBS · PDBe 6YBS · UniProt O15371 · UniProt P63244 · UniProt P62857 · UniProt P08708 · UniProt P60866 · UniProt O75821 · UniProt P46783 · UniProt P25398 · UniProt P62273 · UniProt P62841 · UniProt P23396 · UniProt P39019 · UniProt P62851 · UniProt P62269 · UniProt P46782 · UniProt P62979 · UniProt P62249
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