Research workbench
Structure of the 30S pre-initiation complex 1 (30S ic-1) stalled by GE81112
Analyse Structure of the 30S pre-initiation complex 1 (30S ic-1) stalled by GE81112 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ME0
- Type
- protein + RNA
- Length
- 4,732 residues
- Chains
- 26
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S ribosomal RNA; 30S ribosomal protein S2; 30S ribosomal protein S3; 30S ribosomal…
- UniProt
- P0A7V0, P0A7V3, P0A7V8, P0A7W1, P02358, P02359, P0A7W7, P0A7X3, P0A7R5, P0A7R9, P0A7S3, P0A7S9, P0AG59, P0ADZ4, A0A0U4BH30, P0AG63, P0A7T7, P0A7U3, P0A7U7, P68679, Q5SHR1, P0A705, P03000, P0A707
- Ligands
- FME
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 26 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S ribosomal RNA | rna | 1534 | — | — |
| B | 30S ribosomal protein S2 | protein | 224 | 49% helix, 14% strand | P0A7V0 |
| C | 30S ribosomal protein S3 | protein | 206 | 37% helix, 28% strand | P0A7V3 |
| D | 30S ribosomal protein S4 | protein | 205 | 44% helix, 10% strand | P0A7V8 |
| E | 30S ribosomal protein S5 | protein | 155 | 29% helix, 40% strand | P0A7W1 |
| F | 30S ribosomal protein S6 | protein | 106 | 36% helix, 37% strand | P02358 |
| G | 30S ribosomal protein S7 | protein | 151 | 58% helix, 9% strand | P02359 |
| H | 30S ribosomal protein S8 | protein | 129 | 30% helix, 32% strand | P0A7W7 |
| I | 30S ribosomal protein S9 | protein | 127 | 30% helix, 24% strand | P0A7X3 |
| J | 30S ribosomal protein S10 | protein | 99 | 24% helix, 44% strand | P0A7R5 |
| K | 30S ribosomal protein S11 | protein | 117 | 20% helix, 30% strand | P0A7R9 |
| L | 30S ribosomal protein S12 | protein | 123 | 10% helix, 28% strand | P0A7S3 |
| M | 30S ribosomal protein S13 | protein | 114 | 50% helix, 2% strand | P0A7S9 |
| N | 30S ribosomal protein S14 | protein | 100 | 48% helix, 7% strand | P0AG59 |
| O | 30S ribosomal protein S15 | protein | 88 | 75% helix, 0% strand | P0ADZ4 |
| P | 30S ribosomal protein S16 | protein | 82 | 27% helix, 38% strand | A0A0U4BH30 |
| Q | 30S ribosomal protein S17 | protein | 80 | 4% helix, 56% strand | P0AG63 |
| R | 30S ribosomal protein S18 | protein | 55 | 45% helix, 4% strand | P0A7T7 |
| S | 30S ribosomal protein S19 | protein | 79 | 28% helix, 19% strand | P0A7U3 |
| T | 30S ribosomal protein S20 | protein | 86 | 83% helix, 0% strand | P0A7U7 |
| U | 30S ribosomal protein S21 | protein | 56 | 66% helix, 5% strand | P68679 |
| V | Translation initiation factor if-1 | protein | 71 | 7% helix, 23% strand | Q5SHR1 |
| W | Translation initiation factor if-2 | protein | 501 | 24% helix, 29% strand | P0A705 |
| Y | Translation initiation factor if-3 | protein | 76 | 36% helix, 30% strand | P03000 |
| Z | Translation initiation factor if-3 | protein | 91 | 31% helix, 25% strand | P0A707 |
| X | Fmet-tRNA | rna | 77 | — | — |
Ligands and binding sites
- FME · N-formylmethionine · ligand · chains W, X
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 | 946 | 0.86 | 0.89 | 68 | empty |
| 2 | 931 | 0.84 | 0.87 | 84 | empty |
| 3 | 837 | 0.84 | 0.87 | 69 | empty |
| 4 | 533 | 0.83 | 0.90 | 51 | empty |
| 5 | 554 | 0.82 | 0.89 | 59 | empty |
Interfaces
55 interfaces between chains.
- A–L · 3229 Ų buried · 83 hydrogen bonds · protein-nucleic
- A–D · 3095 Ų buried · 92 hydrogen bonds · protein-nucleic
- A–I · 2917 Ų buried · 88 hydrogen bonds · protein-nucleic
- A–T · 2435 Ų buried · 52 hydrogen bonds · protein-nucleic
- A–N · 2273 Ų buried · 62 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 16 modified, 1 covalent, 1 disulfide (nucleotide modification, covalent ligand, disulfide, nonstandard).
Compared structures
- 5ME0 · Structure of the 30S Pre-Initiation Complex 1 (30S IC-1) Stalled by GE81112 · the same entry in another collection · chain J against J, 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 P0A7V0
- Every structure of UniProt P0A7V3
- Every structure of UniProt P0A7V8
- Every structure of UniProt P0A7W1
- Every structure of UniProt P02358
- Every structure of UniProt P02359
- Every structure of UniProt P0A7W7
- Every structure of UniProt P0A7X3
- Every structure of UniProt P0A7R5
- Every structure of UniProt P0A7R9
- Every structure of UniProt P0A7S3
- Every structure of UniProt P0A7S9
- Every structure of UniProt P0AG59
- Every structure of UniProt P0ADZ4
- Every structure of UniProt A0A0U4BH30
- Every structure of UniProt P0AG63
- Every structure of UniProt P0A7T7
- Every structure of UniProt P0A7U3
- Every structure of UniProt P0A7U7
- Every structure of UniProt P68679
- Every structure of UniProt Q5SHR1
- Every structure of UniProt P0A705
- Every structure of UniProt P03000
- Every structure of UniProt P0A707
- Elsewhere: RCSB PDB 5ME0 · PDBe 5ME0 · UniProt P0A7V0 · UniProt P0A7V3 · UniProt P0A7V8 · UniProt P0A7W1 · UniProt P02358 · UniProt P02359 · UniProt P0A7W7 · UniProt P0A7X3 · UniProt P0A7R5 · UniProt P0A7R9 · UniProt P0A7S3 · UniProt P0A7S9 · UniProt P0AG59 · UniProt P0ADZ4 · UniProt A0A0U4BH30 · UniProt P0AG63 · UniProt P0A7T7 · UniProt P0A7U3 · UniProt P0A7U7 · UniProt P68679 · UniProt Q5SHR1 · UniProt P0A705 · UniProt P03000 · UniProt P0A707
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.