Research workbench
IC2A model of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of AIF1 in P. abyssi
Analyse IC2A 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
- 6SW9
- Type
- protein + RNA
- Length
- 6,100 residues
- Chains
- 35
- 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, Q9V109, Q9V1V0, Q9UZL4, Q9V195, Q9V0V6, P62010, P61994, Q9V1A0, P62012, Q9V2K9, Q9V1U5, Q9V0G0, Q9V1T9, Q9V0G8, Q9UY20, Q9UXZ3, P61029, P61238, Q9V1U1, P62008, Q9V138, Q980A5, Q97W59, Q97Z79
- Ligands
- MET, GNP, MG, ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 35 distinct chains · 25% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 2 | 16S ribosomal RNA | rna | 1497 | — | — |
| A | 30S ribosomal protein S3AE | protein | 188 | 25% helix, 34% strand | Q9V2K7 |
| B | 30S ribosomal protein S2 | protein | 196 | 32% helix, 14% strand | Q9V191 |
| C | Zn-ribbon RNA-binding protein involved in translation | protein | 61 | 8% helix, 16% strand | G8ZFK7 |
| D | 30S ribosomal protein S4 | protein | 175 | 46% helix, 3% strand | P61992 |
| E | 30S ribosomal protein S4E | protein | 242 | 6% helix, 28% strand | Q9V1U8 |
| F | 30S ribosomal protein S5 | protein | 229 | 27% helix, 22% strand | Q9V1V5 |
| G | 30S ribosomal protein S6E | protein | 124 | 8% helix, 33% strand | Q9UYS3 |
| H | 30S ribosomal protein S7 | protein | 213 | 41% helix, 8% strand | Q9V109 |
| I | 30S ribosomal protein S8 | protein | 129 | 27% helix, 12% strand | Q9V1V0 |
| J | 30S ribosomal protein S8E | protein | 126 | 8% helix, 21% strand | Q9UZL4 |
| K | 30S ribosomal protein S9 | protein | 134 | 30% helix, 19% strand | Q9V195 |
| L | 30S ribosomal protein S10 | protein | 101 | 20% helix, 34% strand | Q9V0V6 |
| M | 30S ribosomal protein S11 | protein | 128 | 22% helix, 21% strand | P62010 |
| N | 30S ribosomal protein S12 | protein | 146 | 18% helix, 23% strand | P61994 |
| O | 30S ribosomal protein S13 | protein | 138 | 40% helix, 9% strand | Q9V1A0 |
| P | 30S ribosomal protein S14 type Z | protein | 55 | 13% helix, 2% strand | P62012 |
| Q | 30S ribosomal protein S15 | protein | 152 | 41% helix, 1% strand | Q9V2K9 |
| R | 30S ribosomal protein S17 | protein | 109 | 3% helix, 33% strand | Q9V1U5 |
| S | 30S ribosomal protein S17E | protein | 66 | 59% helix, 0% strand | Q9V0G0 |
| T | 30S ribosomal protein S19 | protein | 125 | 23% helix, 10% strand | Q9V1T9 |
| U | 30S ribosomal protein S19E | protein | 149 | 41% helix, 7% strand | Q9V0G8 |
| V | 30S ribosomal protein S24E | protein | 94 | 22% helix, 37% strand | Q9UY20 |
| W | 30S ribosomal protein S27E | protein | 63 | 0% helix, 11% strand | Q9UXZ3 |
| X | 30S ribosomal protein S28E | protein | 67 | 0% helix, 40% strand | P61029 |
| Y | 30S ribosomal protein S27AE | protein | 50 | 0% helix, 4% strand | P61238 |
| Z | 30S ribosomal protein S3 | protein | 197 | 35% helix, 15% strand | Q9V1U1 |
| 0 | 50S ribosomal protein L41E | protein | 36 | 44% helix, 0% strand | — |
| 3 | 50S ribosomal protein L7AE | protein | 123 | 35% helix, 10% strand | P62008 |
| 5 | MRNA | rna | 20 | — | — |
| 4 | Initiator met-tRNA fmet from E. COLI (A1U72 variant) | rna | 76 | — | — |
| 6 | Translation initiation factor 1A | protein | 95 | 8% helix, 27% strand | Q9V138 |
| 7 | Translation initiation factor 2 subunit gamma | protein | 414 | 15% helix, 31% strand | Q980A5 |
| 8 | Translation initiation factor 2 subunit beta | protein | 129 | 36% helix, 19% strand | Q97W59 |
| 9 | Translation initiation factor 2 subunit alpha | protein | 253 | 38% helix, 24% strand | Q97Z79 |
Ligands and binding sites
- MET · Methionine · ligand · chains 4, 7
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains 7
- MG · Magnesium ion · metal · 34 copies · chains 2, 5, 4, 7
- ZN · Zinc ion · metal · 6 copies · chains C, F, P, 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 | 1042 | 0.86 | 0.88 | 97 | empty |
| 2 | 955 | 0.86 | 0.88 | 70 | empty |
| 3 | 858 | 0.85 | 0.88 | 81 | empty |
| 4 | 570 | 0.84 | 0.91 | 57 | empty |
| 5 | 929 | 0.84 | 0.86 | 92 | empty |
Interfaces
82 interfaces between chains.
- 2–E · 3953 Ų buried · 54 hydrogen bonds · protein-nucleic
- 2–N · 3220 Ų buried · 39 hydrogen bonds · protein-nucleic
- 2–J · 3093 Ų buried · 59 hydrogen bonds · protein-nucleic
- 2–U · 3031 Ų buried · 62 hydrogen bonds · protein-nucleic
- 2–Q · 3004 Ų buried · 42 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 48 modified, 10 disulfide (nucleotide modification, disulfide).
Compared structures
- 6SW9 · IC2A model of cryo-EM structure of a full archaeal ribosomal translation initiation… · 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 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 Q9V109
- Every structure of UniProt Q9V1V0
- Every structure of UniProt Q9UZL4
- Every structure of UniProt Q9V195
- Every structure of UniProt Q9V0V6
- Every structure of UniProt P62010
- Every structure of UniProt P61994
- Every structure of UniProt Q9V1A0
- Every structure of UniProt P62012
- Every structure of UniProt Q9V2K9
- Every structure of UniProt Q9V1U5
- Every structure of UniProt Q9V0G0
- Every structure of UniProt Q9V1T9
- Every structure of UniProt Q9V0G8
- Every structure of UniProt Q9UY20
- Every structure of UniProt Q9UXZ3
- 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
- Every structure of UniProt Q980A5
- Every structure of UniProt Q97W59
- Every structure of UniProt Q97Z79
- Elsewhere: RCSB PDB 6SW9 · PDBe 6SW9 · UniProt Q9V2K7 · UniProt Q9V191 · UniProt G8ZFK7 · UniProt P61992 · UniProt Q9V1U8 · UniProt Q9V1V5 · UniProt Q9UYS3 · UniProt Q9V109 · UniProt Q9V1V0 · UniProt Q9UZL4 · UniProt Q9V195 · UniProt Q9V0V6 · UniProt P62010 · UniProt P61994 · UniProt Q9V1A0 · UniProt P62012 · UniProt Q9V2K9 · UniProt Q9V1U5 · UniProt Q9V0G0 · UniProt Q9V1T9 · UniProt Q9V0G8 · UniProt Q9UY20 · UniProt Q9UXZ3 · UniProt P61029 · UniProt P61238 · UniProt Q9V1U1 · UniProt P62008 · UniProt Q9V138 · UniProt Q980A5 · UniProt Q97W59 · UniProt Q97Z79
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