Research workbench
Small subunit of mycobacterium smegmatis ribosome
Analyse Small subunit of mycobacterium smegmatis ribosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XYU
- Type
- protein + RNA
- Length
- 3,345 residues
- Chains
- 20
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S RNA; 30S ribosomal protein S3; 30S ribosomal protein S4; 30S ribosomal protein S5…
- UniProt
- A0QSD7, A0QSL7, A0QSG6, A0R7F9, A0QS97, A0QSG3, A0QSP9, A0QSD0, A0QSL6, A0QS96, A0QSL5, A0QSG2, A0QVQ3, A0QV37, A0QSE0, A0R7F7, A0QSD5, A0R102, A0QR10
- Ligands
- MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 20 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S RNA | rna | 1379 | — | — |
| C | 30S ribosomal protein S3 | protein | 185 | 31% helix, 24% strand | A0QSD7 |
| D | 30S ribosomal protein S4 | protein | 138 | 46% helix, 7% strand | A0QSL7 |
| E | 30S ribosomal protein S5 | protein | 159 | 26% helix, 28% strand | A0QSG6 |
| F | 30S ribosomal protein S6 | protein | 67 | 19% helix, 21% strand | A0R7F9 |
| G | 30S ribosomal protein S7 | protein | 144 | 59% helix, 6% strand | A0QS97 |
| H | 30S ribosomal protein S8 | protein | 129 | 26% helix, 28% strand | A0QSG3 |
| I | 30S ribosomal protein S9 | protein | 124 | 35% helix, 17% strand | A0QSP9 |
| J | 30S ribosomal protein S10 | protein | 97 | 28% helix, 29% strand | A0QSD0 |
| K | 30S ribosomal protein S11 | protein | 115 | 30% helix, 25% strand | A0QSL6 |
| L | 30S ribosomal protein S12 | protein | 123 | 5% helix, 18% strand | A0QS96 |
| M | 30S ribosomal protein S13 | protein | 112 | 49% helix, 2% strand | A0QSL5 |
| N | 30S ribosomal protein S14 type Z | protein | 60 | 27% helix, 8% strand | A0QSG2 |
| O | 30S ribosomal protein S15 | protein | 86 | 79% helix, 0% strand | A0QVQ3 |
| P | 30S ribosomal protein S16 | protein | 94 | 28% helix, 23% strand | A0QV37 |
| Q | 30S ribosomal protein S17 | protein | 91 | 0% helix, 58% strand | A0QSE0 |
| R | 30S ribosomal protein S18 2 | protein | 55 | 51% helix, 4% strand | A0R7F7 |
| S | 30S ribosomal protein S19 | protein | 79 | 25% helix, 20% strand | A0QSD5 |
| T | 30S ribosomal protein S20 | protein | 83 | 86% helix, 0% strand | A0R102 |
| U | Conserved domain protein | protein | 25 | 72% helix, 0% strand | A0QR10 |
Ligands and binding sites
- MG · Magnesium ion · metal · 48 copies · chains A, T, S
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 | 1070 | 0.86 | 0.88 | 85 | MG |
| 2 | 1021 | 0.86 | 0.87 | 84 | empty |
| 3 | 1110 | 0.85 | 0.86 | 82 | MG |
| 4 | 998 | 0.84 | 0.85 | 81 | MG |
| 5 | 1084 | 0.83 | 0.84 | 80 | empty |
Interfaces
35 interfaces between chains.
- A–L · 3157 Ų buried · 75 hydrogen bonds · protein-nucleic
- A–I · 2874 Ų buried · 55 hydrogen bonds · protein-nucleic
- A–Q · 2734 Ų buried · 51 hydrogen bonds · protein-nucleic
- A–T · 2440 Ų buried · 54 hydrogen bonds · protein-nucleic
- A–D · 2225 Ų buried · 34 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5XYU · Small subunit of Mycobacterium smegmatis ribosome · the same entry in another collection · chain K against K, 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 A0QSD7
- Every structure of UniProt A0QSL7
- Every structure of UniProt A0QSG6
- Every structure of UniProt A0R7F9
- 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 A0QR10
- Elsewhere: RCSB PDB 5XYU · PDBe 5XYU · UniProt A0QSD7 · UniProt A0QSL7 · UniProt A0QSG6 · UniProt A0R7F9 · 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 A0QR10
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