Research workbench
IC2 head of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of AIF1 in P. abyssi
Analyse IC2 head of cryo-EM structure of a full archaeal ribosomal translation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SWE
- Type
- protein + RNA
- Length
- 2,009 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S ribosomal RNA; 30S ribosomal protein S7; 30S ribosomal protein S9; 30S ribosomal…
- UniProt
- Q9V109, Q9V195, Q9V0V6, Q9V1A0, P62012, Q9V0G0, Q9V1T9, Q9V0G8, P61029, P61238, Q9V1U1, P62008, Q9V138
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 15 distinct chains · 31% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 2 | 16S ribosomal RNA | rna | 468 | — | — |
| H | 30S ribosomal protein S7 | protein | 213 | 39% helix, 7% strand | Q9V109 |
| K | 30S ribosomal protein S9 | protein | 134 | 31% helix, 22% strand | Q9V195 |
| L | 30S ribosomal protein S10 | protein | 101 | 23% helix, 39% strand | Q9V0V6 |
| O | 30S ribosomal protein S13 | protein | 143 | 41% helix, 8% strand | Q9V1A0 |
| P | 30S ribosomal protein S14 type Z | protein | 55 | 20% helix, 9% strand | P62012 |
| S | 30S ribosomal protein S17E | protein | 66 | 50% helix, 0% strand | Q9V0G0 |
| T | 30S ribosomal protein S19 | protein | 130 | 23% helix, 11% strand | Q9V1T9 |
| U | 30S ribosomal protein S19E | protein | 149 | 45% helix, 10% strand | Q9V0G8 |
| X | 30S ribosomal protein S28E | protein | 67 | 0% helix, 45% strand | P61029 |
| Y | 30S ribosomal protein S27AE | protein | 50 | 0% helix, 8% strand | P61238 |
| Z | 30S ribosomal protein S3 | protein | 197 | 35% helix, 21% strand | Q9V1U1 |
| 3 | 50S ribosomal protein L7AE | protein | 123 | 37% helix, 11% strand | P62008 |
| 4 | Initiator met-tRNA fmet from E. COLI (A1U72 variant) | rna | 18 | — | — |
| 6 | Translation initiation factor 1A | protein | 95 | 17% helix, 22% strand | Q9V138 |
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 | 1037 | 0.87 | 0.88 | 93 | empty |
| 2 | 1055 | 0.86 | 0.88 | 74 | empty |
| 3 | 627 | 0.85 | 0.91 | 70 | MG |
| 4 | 911 | 0.81 | 0.84 | 64 | MG |
| 5 | 323 | 0.78 | 0.90 | 35 | empty |
Interfaces
31 interfaces between chains.
- 2–U · 3084 Ų buried · 48 hydrogen bonds · protein-nucleic
- 2–K · 2850 Ų buried · 38 hydrogen bonds · protein-nucleic
- 2–H · 2565 Ų buried · 53 hydrogen bonds · protein-nucleic
- 2–O · 2261 Ų buried · 40 hydrogen bonds · protein-nucleic
- 2–T · 2057 Ų buried · 43 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 11 modified, 1 disulfide (nucleotide modification, disulfide).
Compared structures
- 6SWE · IC2 head of cryo-EM structure of a full archaeal ribosomal translation initiation complex… · the same entry in another collection · chain Y against Y, 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 Q9V109
- Every structure of UniProt Q9V195
- Every structure of UniProt Q9V0V6
- Every structure of UniProt Q9V1A0
- Every structure of UniProt P62012
- Every structure of UniProt Q9V0G0
- Every structure of UniProt Q9V1T9
- Every structure of UniProt Q9V0G8
- Every structure of UniProt P61029
- Every structure of UniProt P61238
- Every structure of UniProt Q9V1U1
- Every structure of UniProt P62008
- Every structure of UniProt Q9V138
- Elsewhere: RCSB PDB 6SWE · PDBe 6SWE · UniProt Q9V109 · UniProt Q9V195 · UniProt Q9V0V6 · UniProt Q9V1A0 · UniProt P62012 · UniProt Q9V0G0 · UniProt Q9V1T9 · UniProt Q9V0G8 · UniProt P61029 · UniProt P61238 · UniProt Q9V1U1 · UniProt P62008 · UniProt Q9V138
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.