Research workbench
Staphylococcus aureus 30S ribosomal subunit in presence of spermidine (body only)
Analyse Staphylococcus aureus 30S ribosomal subunit in presence of spermidine (body… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BGD
- Type
- protein + RNA
- Length
- 2,538 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRNA; 16S ribosomal RNA; 30S ribosomal protein S2; 30S ribosomal protein S4; 30S…
- UniProt
- Q2FZ25, Q2FXK6, Q2FW23, Q2G113, Q2FW20, Q2FW31, P0A0H0, Q2G2Q1, Q2FZ45, Q2FW15, Q2G111, Q2FXY6
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 14 distinct chains · 29% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MRNA | rna | 32 | — | — |
| a | 16S ribosomal RNA | rna | 1096 | — | — |
| b | 30S ribosomal protein S2 | protein | 163 | 26% helix, 15% strand | Q2FZ25 |
| d | 30S ribosomal protein S4 | protein | 196 | 36% helix, 9% strand | Q2FXK6 |
| e | 30S ribosomal protein S5 | protein | 157 | 24% helix, 29% strand | Q2FW23 |
| f | 30S ribosomal protein S6 | protein | 96 | 25% helix, 35% strand | Q2G113 |
| h | 30S ribosomal protein S8 | protein | 131 | 27% helix, 27% strand | Q2FW20 |
| k | 30S ribosomal protein S11 | protein | 118 | 30% helix, 26% strand | Q2FW31 |
| l | 30S ribosomal protein S12 | protein | 135 | 3% helix, 23% strand | P0A0H0 |
| o | 30S ribosomal protein S15 | protein | 88 | 70% helix, 0% strand | Q2G2Q1 |
| p | 30S ribosomal protein S16 | protein | 90 | 29% helix, 27% strand | Q2FZ45 |
| q | 30S ribosomal protein S17 | protein | 86 | 0% helix, 50% strand | Q2FW15 |
| r | 30S ribosomal protein S18 | protein | 70 | 34% helix, 3% strand | Q2G111 |
| t | 30S ribosomal protein S20 | protein | 80 | 63% helix, 0% strand | Q2FXY6 |
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 | 573 | 0.83 | 0.90 | 52 | empty |
| 2 | 681 | 0.81 | 0.87 | 59 | empty |
| 3 | 386 | 0.79 | 0.89 | 44 | empty |
| 4 | 381 | 0.79 | 0.89 | 45 | empty |
| 5 | 683 | 0.78 | 0.84 | 55 | empty |
Interfaces
25 interfaces between chains.
- a–l · 3581 Ų buried · 95 hydrogen bonds · protein-nucleic
- a–d · 2991 Ų buried · 76 hydrogen bonds · protein-nucleic
- a–p · 2650 Ų buried · 55 hydrogen bonds · protein-nucleic
- a–t · 2452 Ų buried · 50 hydrogen bonds · protein-nucleic
- a–q · 2319 Ų buried · 55 hydrogen bonds · protein-nucleic
Compared structures
- 7BGD · Staphylococcus aureus 30S ribosomal subunit in presence of spermidine (body only) · the same entry in another collection · chain p against p, 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 Q2FZ25
- Every structure of UniProt Q2FXK6
- Every structure of UniProt Q2FW23
- Every structure of UniProt Q2G113
- Every structure of UniProt Q2FW20
- Every structure of UniProt Q2FW31
- Every structure of UniProt P0A0H0
- Every structure of UniProt Q2G2Q1
- Every structure of UniProt Q2FZ45
- Every structure of UniProt Q2FW15
- Every structure of UniProt Q2G111
- Every structure of UniProt Q2FXY6
- Elsewhere: RCSB PDB 7BGD · PDBe 7BGD · UniProt Q2FZ25 · UniProt Q2FXK6 · UniProt Q2FW23 · UniProt Q2G113 · UniProt Q2FW20 · UniProt Q2FW31 · UniProt P0A0H0 · UniProt Q2G2Q1 · UniProt Q2FZ45 · UniProt Q2FW15 · UniProt Q2G111 · UniProt Q2FXY6
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