MolNFT v1 · #160826 · protein + RNA
Bacterial 45SRBGA ribosomal particle class a
6PVK · 23S rRNA: “Bacterial 45SRBGA ribosomal particle class a”. Electron microscopy, 20 pockets (best druggability 0.88). MolNFT v1 #160826 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6PVK
- Type
- protein + RNA
- Length
- 3,960 residues
- Chains
- 17
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S rRNA; 50S ribosomal protein L2; 50S ribosomal protein L3; 50S ribosomal protein L4…
- UniProt
- A0A063XCB6, A0A063X745, A0A063X8U6, A0A063XCH0, A0A063X754, A0A063XCP1, A0A063XCG5, A0A063XHU6, A0A063XFC1, A0A063XIS2, F5HRT3, A0A063XB36, F5HRS7, A0A3A5I502, F5HRV8, A0A063XCT1
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 17 distinct chains · 21% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 23S rRNA | rna | 2169 | — | — |
| C | 50S ribosomal protein L2 | protein | 220 | 7% helix, 26% strand | A0A063XCB6 |
| D | 50S ribosomal protein L3 | protein | 167 | 9% helix, 36% strand | A0A063X745 |
| E | 50S ribosomal protein L4 | protein | 183 | 30% helix, 8% strand | A0A063X8U6 |
| J | 50S ribosomal protein L13 | protein | 141 | 30% helix, 13% strand | A0A063XCH0 |
| K | 50S ribosomal protein L14 | protein | 116 | 5% helix, 22% strand | A0A063X754 |
| L | 50S ribosomal protein L15 | protein | 97 | 16% helix, 4% strand | A0A063XCP1 |
| N | 50S ribosomal protein L17 | protein | 119 | 33% helix, 19% strand | A0A063XCG5 |
| P | 50S ribosomal protein L19 | protein | 98 | 8% helix, 39% strand | A0A063XHU6 |
| Q | 50S ribosomal protein L20 | protein | 116 | 47% helix, 0% strand | A0A063XFC1 |
| R | 50S ribosomal protein L21 | protein | 100 | 0% helix, 45% strand | A0A063XIS2 |
| S | 50S ribosomal protein L22 | protein | 101 | 22% helix, 34% strand | F5HRT3 |
| T | 50S ribosomal protein L23 | protein | 89 | 26% helix, 39% strand | A0A063XB36 |
| U | 50S ribosomal protein L24 | protein | 90 | 3% helix, 31% strand | F5HRS7 |
| b | 50S ribosomal protein L32 | protein | 52 | 13% helix, 12% strand | A0A3A5I502 |
| Y | 50S ribosomal protein L29 | protein | 63 | 75% helix, 0% strand | F5HRV8 |
| d | 50S ribosomal protein L34 | protein | 39 | 56% 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 | 1169 | 0.88 | 0.91 | 109 | empty |
| 2 | 779 | 0.85 | 0.88 | 69 | empty |
| 3 | 1142 | 0.83 | 0.85 | 93 | empty |
| 4 | 721 | 0.83 | 0.87 | 67 | empty |
| 5 | 558 | 0.83 | 0.89 | 53 | empty |
Interfaces
29 interfaces between chains.
- A–C · 4962 Ų buried · 83 hydrogen bonds · protein-nucleic
- A–Q · 4088 Ų buried · 57 hydrogen bonds · protein-nucleic
- A–E · 3665 Ų buried · 60 hydrogen bonds · protein-nucleic
- A–N · 2989 Ų buried · 54 hydrogen bonds · protein-nucleic
- A–D · 2806 Ų buried · 47 hydrogen bonds · protein-nucleic
Compared structures
- 6PVK · Bacterial 45SRbgA ribosomal particle class A · 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 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 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 A0A3A5I502
- Every structure of UniProt F5HRV8
- Every structure of UniProt A0A063XCT1
- Elsewhere: RCSB PDB 6PVK · PDBe 6PVK · UniProt A0A063XCB6 · UniProt A0A063X745 · UniProt A0A063X8U6 · UniProt A0A063XCH0 · UniProt A0A063X754 · UniProt A0A063XCP1 · UniProt A0A063XCG5 · UniProt A0A063XHU6 · UniProt A0A063XFC1 · UniProt A0A063XIS2 · UniProt F5HRT3 · UniProt A0A063XB36 · UniProt F5HRS7 · UniProt A0A3A5I502 · UniProt F5HRV8 · UniProt A0A063XCT1
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