Research workbench
Structure of the 30S small ribosomal subunit from mycobacterium smegmatis
Analyse Structure of the 30S small ribosomal subunit from mycobacterium smegmatis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O5J
- Type
- protein + RNA
- Length
- 3,942 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S rRNA; Conserved domain protein; 30S ribosomal protein S3; 30S ribosomal protein S4…
- UniProt
- A0QR10, A0QSD7, A0QSL7, A0QSG6, A0A0D6J3X3, A0QS97, A0QSG3, A0QSP9, A0QSD0, A0QSL6, A0QS96, A0QSL5, A0QSG2, A0QVQ3, A0QV37, A0QSE0, A0R7F7, A0QSD5, A0R102, A0QVB8, A0R215
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 24 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S rRNA | rna | 1511 | — | — |
| B | Conserved domain protein | protein | 32 | 88% helix, 0% strand | A0QR10 |
| C | 30S ribosomal protein S3 | protein | 208 | 31% helix, 32% strand | A0QSD7 |
| D | 30S ribosomal protein S4 | protein | 200 | 46% helix, 9% strand | A0QSL7 |
| E | 30S ribosomal protein S5 | protein | 180 | 39% helix, 35% strand | A0QSG6 |
| F | 30S ribosomal protein S6 | protein | 96 | 30% helix, 41% strand | A0A0D6J3X3 |
| G | 30S ribosomal protein S7 | protein | 155 | 58% helix, 10% strand | A0QS97 |
| H | 30S ribosomal protein S8 | protein | 131 | 24% helix, 32% strand | A0QSG3 |
| I | 30S ribosomal protein S9 | protein | 126 | 32% helix, 20% strand | A0QSP9 |
| J | 30S ribosomal protein S10 | protein | 99 | 24% helix, 38% strand | A0QSD0 |
| K | 30S ribosomal protein S11 | protein | 115 | 27% helix, 31% strand | A0QSL6 |
| L | 30S ribosomal protein S12 | protein | 122 | 8% helix, 28% strand | A0QS96 |
| M | 30S ribosomal protein S13 | protein | 116 | 53% helix, 3% strand | A0QSL5 |
| N | 30S ribosomal protein S14 type Z | protein | 60 | 33% helix, 8% strand | A0QSG2 |
| O | 30S ribosomal protein S15 | protein | 88 | 76% helix, 0% strand | A0QVQ3 |
| P | 30S ribosomal protein S16 | protein | 113 | 33% helix, 24% strand | A0QV37 |
| Q | 30S ribosomal protein S17 | protein | 94 | 0% helix, 52% strand | A0QSE0 |
| R | 30S ribosomal protein S18 2 | protein | 65 | 40% helix, 3% strand | A0R7F7 |
| S | 30S ribosomal protein S19 | protein | 82 | 27% helix, 20% strand | A0QSD5 |
| T | 30S ribosomal protein S20 | protein | 85 | 86% helix, 0% strand | A0R102 |
| V | 30S ribosomal protein S2 | protein | 228 | 50% helix, 12% strand | A0QVB8 |
| W | TRNA-phe anticodon stem | rna | 19 | — | — |
| X | MRNA fragment | rna | 6 | — | — |
| g | 50S ribosomal protein L31 | protein | 11 | 73% helix, 0% strand | A0R215 |
Ligands and binding sites
- MG · Magnesium ion · metal · 217 copies · chains A, T, O, N, E, P, I, Q, X, K, C, F, R
- ZN · Zinc ion · metal · 2 copies · chains N, R
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 | 1126 | 0.88 | 0.90 | 86 | MG |
| 2 | 1100 | 0.85 | 0.87 | 88 | MG |
| 3 | 861 | 0.85 | 0.88 | 58 | MG |
| 4 | 1092 | 0.84 | 0.86 | 72 | MG |
| 5 | 1116 | 0.84 | 0.85 | 82 | MG |
Interfaces
48 interfaces between chains.
- A–L · 3066 Ų buried · 76 hydrogen bonds · protein-nucleic
- A–D · 2984 Ų buried · 66 hydrogen bonds · protein-nucleic
- A–I · 2945 Ų buried · 72 hydrogen bonds · protein-nucleic
- A–Q · 2686 Ų buried · 52 hydrogen bonds · protein-nucleic
- A–T · 2472 Ų buried · 57 hydrogen bonds · protein-nucleic
Compared structures
- 5O5J · Structure of the 30S small ribosomal subunit from Mycobacterium smegmatis · the same entry in another collection · chain E against E, 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 A0QR10
- Every structure of UniProt A0QSD7
- Every structure of UniProt A0QSL7
- Every structure of UniProt A0QSG6
- Every structure of UniProt A0A0D6J3X3
- Every structure of UniProt A0QS97
- Every structure of UniProt A0QSG3
- Every structure of UniProt A0QSP9
- Every structure of UniProt A0QSD0
- Every structure of UniProt A0QSL6
- Every structure of UniProt A0QS96
- Every structure of UniProt A0QSL5
- Every structure of UniProt A0QSG2
- Every structure of UniProt A0QVQ3
- Every structure of UniProt A0QV37
- Every structure of UniProt A0QSE0
- Every structure of UniProt A0R7F7
- Every structure of UniProt A0QSD5
- Every structure of UniProt A0R102
- Every structure of UniProt A0QVB8
- Every structure of UniProt A0R215
- Elsewhere: RCSB PDB 5O5J · PDBe 5O5J · UniProt A0QR10 · UniProt A0QSD7 · UniProt A0QSL7 · UniProt A0QSG6 · UniProt A0A0D6J3X3 · UniProt A0QS97 · UniProt A0QSG3 · UniProt A0QSP9 · UniProt A0QSD0 · UniProt A0QSL6 · UniProt A0QS96 · UniProt A0QSL5 · UniProt A0QSG2 · UniProt A0QVQ3 · UniProt A0QV37 · UniProt A0QSE0 · UniProt A0R7F7 · UniProt A0QSD5 · UniProt A0R102 · UniProt A0QVB8 · UniProt A0R215
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.