Research workbench
Staphylococcus aureus 30S ribosomal subunit in presence of spermidine (head only)
Analyse Staphylococcus aureus 30S ribosomal subunit in presence of spermidine (head… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BGE
- Type
- protein + RNA
- Length
- 1,344 residues
- Chains
- 9
- 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
- Q2FZ25, Q2FW12, P48940, Q2FW39, Q931G5, Q2FW30, Q2FW19, Q2FW10
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 9 distinct chains · 30% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a | 16S ribosomal RNA | rna | 465 | — | — |
| b | 30S ribosomal protein S2 | protein | 107 | 30% helix, 6% strand | Q2FZ25 |
| c | 30S ribosomal protein S3 | protein | 202 | 31% helix, 27% strand | Q2FW12 |
| g | 30S ribosomal protein S7 | protein | 145 | 54% helix, 3% strand | P48940 |
| i | 30S ribosomal protein S9 | protein | 125 | 24% helix, 16% strand | Q2FW39 |
| j | 30S ribosomal protein S10 | protein | 97 | 24% helix, 33% strand | Q931G5 |
| m | 30S ribosomal protein S13 | protein | 72 | 22% helix, 0% strand | Q2FW30 |
| n | 30S ribosomal protein S14 type Z | protein | 59 | 29% helix, 5% strand | Q2FW19 |
| s | 30S ribosomal protein S19 | protein | 72 | 7% helix, 21% strand | Q2FW10 |
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 | 1113 | 0.86 | 0.88 | 93 | empty |
| 2 | 1088 | 0.84 | 0.86 | 81 | empty |
| 3 | 791 | 0.82 | 0.86 | 52 | empty |
| 4 | 802 | 0.81 | 0.85 | 47 | empty |
| 5 | 603 | 0.78 | 0.85 | 31 | empty |
Interfaces
16 interfaces between chains.
- a–i · 3056 Ų buried · 58 hydrogen bonds · protein-nucleic
- a–m · 2145 Ų buried · 45 hydrogen bonds · protein-nucleic
- a–n · 2136 Ų buried · 38 hydrogen bonds · protein-nucleic
- a–j · 2003 Ų buried · 36 hydrogen bonds · protein-nucleic
- a–g · 1626 Ų buried · 37 hydrogen bonds · protein-nucleic
Compared structures
- 7BGE · Staphylococcus aureus 30S ribosomal subunit in presence of spermidine (head only) · the same entry in another collection · chain s against s, TM-score 1.00
- Q2FW12 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S3 (Q2FW12) · a predicted model of the same protein · chain c against A, TM-score 0.98
- P48940 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S7 (P48940) · a predicted model of the same protein · chain g against A, TM-score 0.97
- Q931G5 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S10 (Q931G5) · a predicted model of the same protein · chain j against A, TM-score 0.95
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 Q2FZ25
- Every structure of UniProt Q2FW12
- Every structure of UniProt P48940
- Every structure of UniProt Q2FW39
- Every structure of UniProt Q931G5
- Every structure of UniProt Q2FW30
- Every structure of UniProt Q2FW19
- Every structure of UniProt Q2FW10
- Elsewhere: RCSB PDB 7BGE · PDBe 7BGE · UniProt Q2FZ25 · UniProt Q2FW12 · UniProt P48940 · UniProt Q2FW39 · UniProt Q931G5 · UniProt Q2FW30 · UniProt Q2FW19 · UniProt Q2FW10
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