Research workbench
Bacterial 45SRBGA ribosomal particle class B
Analyse Bacterial 45SRBGA ribosomal particle class B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PPF
- Type
- protein + RNA
- Length
- 4,684 residues
- Chains
- 21
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S rRNA; 5S rRNA; 50S ribosomal protein L2; 50S ribosomal protein L3; 50S ribosomal…
- UniProt
- A0A063XCB6, A0A063X745, A0A063X8U6, A0A063XCH0, A0A063X754, A0A063XCP1, A0A063XCG5, F5HRS9, A0A063XHU6, A0A063XFC1, A0A063XIS2, F5HRT3, A0A063XB36, F5HRS7, A0A063XF22, F5HRU6, A0A3A5I502, F5HRV8, A0A063XCT1
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 21 distinct chains · 22% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 23S rRNA | rna | 2471 | — | — |
| B | 5S rRNA | rna | 112 | — | — |
| C | 50S ribosomal protein L2 | protein | 221 | 6% helix, 28% strand | A0A063XCB6 |
| D | 50S ribosomal protein L3 | protein | 167 | 5% helix, 36% strand | A0A063X745 |
| E | 50S ribosomal protein L4 | protein | 194 | 33% helix, 8% strand | A0A063X8U6 |
| J | 50S ribosomal protein L13 | protein | 141 | 28% helix, 12% strand | A0A063XCH0 |
| K | 50S ribosomal protein L14 | protein | 122 | 7% helix, 30% strand | A0A063X754 |
| L | 50S ribosomal protein L15 | protein | 128 | 20% helix, 10% strand | A0A063XCP1 |
| N | 50S ribosomal protein L17 | protein | 119 | 41% helix, 18% strand | A0A063XCG5 |
| O | 50S ribosomal protein L18 | protein | 104 | 29% helix, 16% strand | F5HRS9 |
| P | 50S ribosomal protein L19 | protein | 103 | 10% helix, 40% strand | A0A063XHU6 |
| Q | 50S ribosomal protein L20 | protein | 117 | 67% helix, 0% strand | A0A063XFC1 |
| R | 50S ribosomal protein L21 | protein | 96 | 0% helix, 40% strand | A0A063XIS2 |
| S | 50S ribosomal protein L22 | protein | 109 | 29% helix, 24% strand | F5HRT3 |
| T | 50S ribosomal protein L23 | protein | 88 | 27% helix, 32% strand | A0A063XB36 |
| U | 50S ribosomal protein L24 | protein | 98 | 6% helix, 29% strand | F5HRS7 |
| V | 50S ribosomal protein L27 | protein | 73 | 0% helix, 34% strand | A0A063XF22 |
| Z | 50S ribosomal protein L30 | protein | 58 | 31% helix, 22% strand | F5HRU6 |
| b | 50S ribosomal protein L32 | protein | 54 | 7% helix, 11% strand | A0A3A5I502 |
| Y | 50S ribosomal protein L29 | protein | 65 | 66% helix, 0% strand | F5HRV8 |
| d | 50S ribosomal protein L34 | protein | 44 | 39% helix, 0% strand | A0A063XCT1 |
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 | 669 | 0.85 | 0.90 | 73 | empty |
| 2 | 639 | 0.85 | 0.90 | 71 | empty |
| 3 | 1187 | 0.85 | 0.86 | 93 | empty |
| 4 | 529 | 0.83 | 0.90 | 57 | empty |
| 5 | 512 | 0.83 | 0.90 | 52 | empty |
Interfaces
36 interfaces between chains.
- A–C · 4936 Ų buried · 107 hydrogen bonds · protein-nucleic
- A–Q · 4158 Ų buried · 70 hydrogen bonds · protein-nucleic
- A–E · 4041 Ų buried · 69 hydrogen bonds · protein-nucleic
- A–L · 3343 Ų buried · 71 hydrogen bonds · protein-nucleic
- A–N · 2971 Ų buried · 44 hydrogen bonds · protein-nucleic
Compared structures
- 6PPF · Bacterial 45SRbgA ribosomal particle class B · the same entry in another collection · chain A against A, 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 A0A063XCB6
- Every structure of UniProt A0A063X745
- Every structure of UniProt A0A063X8U6
- Every structure of UniProt A0A063XCH0
- Every structure of UniProt A0A063X754
- Every structure of UniProt A0A063XCP1
- Every structure of UniProt A0A063XCG5
- Every structure of UniProt F5HRS9
- Every structure of UniProt A0A063XHU6
- Every structure of UniProt A0A063XFC1
- Every structure of UniProt A0A063XIS2
- Every structure of UniProt F5HRT3
- Every structure of UniProt A0A063XB36
- Every structure of UniProt F5HRS7
- Every structure of UniProt A0A063XF22
- Every structure of UniProt F5HRU6
- Every structure of UniProt A0A3A5I502
- Every structure of UniProt F5HRV8
- Every structure of UniProt A0A063XCT1
- Elsewhere: RCSB PDB 6PPF · PDBe 6PPF · UniProt A0A063XCB6 · UniProt A0A063X745 · UniProt A0A063X8U6 · UniProt A0A063XCH0 · UniProt A0A063X754 · UniProt A0A063XCP1 · UniProt A0A063XCG5 · UniProt F5HRS9 · UniProt A0A063XHU6 · UniProt A0A063XFC1 · UniProt A0A063XIS2 · UniProt F5HRT3 · UniProt A0A063XB36 · UniProt F5HRS7 · UniProt A0A063XF22 · UniProt F5HRU6 · UniProt A0A3A5I502 · UniProt F5HRV8 · UniProt A0A063XCT1
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