Research workbench
IC2 body model of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of AIF1 in P. abyssi
Analyse IC2 body model 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
- 6SWD
- Type
- protein + RNA
- Length
- 3,357 residues
- Chains
- 19
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S ribosomal RNA; 30S ribosomal protein S3AE; 30S ribosomal protein S2; Zn-ribbon…
- UniProt
- Q9V2K7, Q9V191, G8ZFK7, P61992, Q9V1U8, Q9V1V5, Q9UYS3, Q9V1V0, Q9UZL4, P62010, P61994, Q9V2K9, Q9V1U5, Q9UY20, Q9UXZ3, Q9V138
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 19 distinct chains · 21% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 2 | 16S ribosomal RNA | rna | 1044 | — | — |
| A | 30S ribosomal protein S3AE | protein | 188 | 27% helix, 33% strand | Q9V2K7 |
| B | 30S ribosomal protein S2 | protein | 196 | 32% helix, 13% strand | Q9V191 |
| C | Zn-ribbon RNA-binding protein involved in translation | protein | 61 | 8% helix, 20% strand | G8ZFK7 |
| D | 30S ribosomal protein S4 | protein | 175 | 41% helix, 5% strand | P61992 |
| E | 30S ribosomal protein S4E | protein | 242 | 5% helix, 33% strand | Q9V1U8 |
| F | 30S ribosomal protein S5 | protein | 229 | 31% helix, 26% strand | Q9V1V5 |
| G | 30S ribosomal protein S6E | protein | 124 | 6% helix, 35% strand | Q9UYS3 |
| I | 30S ribosomal protein S8 | protein | 129 | 29% helix, 30% strand | Q9V1V0 |
| J | 30S ribosomal protein S8E | protein | 126 | 9% helix, 31% strand | Q9UZL4 |
| M | 30S ribosomal protein S11 | protein | 128 | 19% helix, 23% strand | P62010 |
| N | 30S ribosomal protein S12 | protein | 146 | 21% helix, 29% strand | P61994 |
| Q | 30S ribosomal protein S15 | protein | 152 | 39% helix, 5% strand | Q9V2K9 |
| R | 30S ribosomal protein S17 | protein | 109 | 0% helix, 39% strand | Q9V1U5 |
| V | 30S ribosomal protein S24E | protein | 94 | 26% helix, 34% strand | Q9UY20 |
| W | 30S ribosomal protein S27E | protein | 63 | 0% helix, 17% strand | Q9UXZ3 |
| 0 | 30S ribosomal protein AL41 | protein | 36 | 44% helix, 0% strand | — |
| 5 | MRNA | rna | 20 | — | — |
| 6 | Translation initiation factor 1A | protein | 95 | 7% helix, 26% strand | Q9V138 |
Ligands and binding sites
- MG · Magnesium ion · metal · 25 copies · chains 2, 5
- ZN · Zinc ion · metal · 5 copies · chains C, F, R, W
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 | 1017 | 0.85 | 0.87 | 69 | empty |
| 2 | 1007 | 0.85 | 0.87 | 72 | MG |
| 3 | 1013 | 0.85 | 0.86 | 86 | empty |
| 4 | 1096 | 0.84 | 0.86 | 91 | empty |
| 5 | 824 | 0.84 | 0.87 | 73 | MG |
Interfaces
40 interfaces between chains.
- 2–E · 3994 Ų buried · 52 hydrogen bonds · protein-nucleic
- 2–N · 3447 Ų buried · 48 hydrogen bonds · protein-nucleic
- 2–J · 3253 Ų buried · 50 hydrogen bonds · protein-nucleic
- 2–Q · 3169 Ų buried · 56 hydrogen bonds · protein-nucleic
- 2–D · 3074 Ų buried · 42 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 32 modified, 4 disulfide (nucleotide modification, disulfide).
Compared structures
- 6SWD · IC2 body model of cryo-EM structure of a full archaeal ribosomal translation initiation… · the same entry in another collection · chain N against N, 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 Q9V2K7
- Every structure of UniProt Q9V191
- Every structure of UniProt G8ZFK7
- Every structure of UniProt P61992
- Every structure of UniProt Q9V1U8
- Every structure of UniProt Q9V1V5
- Every structure of UniProt Q9UYS3
- Every structure of UniProt Q9V1V0
- Every structure of UniProt Q9UZL4
- Every structure of UniProt P62010
- Every structure of UniProt P61994
- Every structure of UniProt Q9V2K9
- Every structure of UniProt Q9V1U5
- Every structure of UniProt Q9UY20
- Every structure of UniProt Q9UXZ3
- Every structure of UniProt Q9V138
- Elsewhere: RCSB PDB 6SWD · PDBe 6SWD · UniProt Q9V2K7 · UniProt Q9V191 · UniProt G8ZFK7 · UniProt P61992 · UniProt Q9V1U8 · UniProt Q9V1V5 · UniProt Q9UYS3 · UniProt Q9V1V0 · UniProt Q9UZL4 · UniProt P62010 · UniProt P61994 · UniProt Q9V2K9 · UniProt Q9V1U5 · UniProt Q9UY20 · UniProt Q9UXZ3 · UniProt Q9V138
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