Research workbench
50S ribosomal subunit assembly intermediate state 2
Analyse 50S ribosomal subunit assembly intermediate state 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GC6
- Type
- protein + RNA
- Length
- 4,210 residues
- Chains
- 19
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S ribosomal RNA; 50S ribosomal protein L2; 50S ribosomal protein L3; 50S ribosomal…
- UniProt
- P60422, P60438, P60723, P0AG55, P0AA10, P0ADY3, P02413, P0AG44, P0A7K6, P0A7L3, P0AG48, P61175, P0ADZ0, P60624, P0A7M6, P0A7N4, P0A7P5, P0AG51
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 19 distinct chains · 23% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 23S ribosomal RNA | rna | 2092 | — | — |
| C | 50S ribosomal protein L2 | protein | 204 | 5% helix, 28% strand | P60422 |
| D | 50S ribosomal protein L3 | protein | 182 | 7% helix, 38% strand | P60438 |
| E | 50S ribosomal protein L4 | protein | 201 | 28% helix, 8% strand | P60723 |
| G | 50S ribosomal protein L6 | protein | 176 | 18% helix, 21% strand | P0AG55 |
| J | 50S ribosomal protein L13 | protein | 142 | 32% helix, 18% strand | P0AA10 |
| K | 50S ribosomal protein L14 | protein | 122 | 0% helix, 35% strand | P0ADY3 |
| L | 50S ribosomal protein L15 | protein | 109 | 10% helix, 6% strand | P02413 |
| N | 50S ribosomal protein L17 | protein | 120 | 43% helix, 13% strand | P0AG44 |
| P | 50S ribosomal protein L19 | protein | 114 | 17% helix, 43% strand | P0A7K6 |
| Q | 50S ribosomal protein L20 | protein | 117 | 75% helix, 0% strand | P0A7L3 |
| R | 50S ribosomal protein L21 | protein | 103 | 0% helix, 52% strand | P0AG48 |
| S | 50S ribosomal protein L22 | protein | 110 | 35% helix, 33% strand | P61175 |
| T | 50S ribosomal protein L23 | protein | 93 | 26% helix, 27% strand | P0ADZ0 |
| U | 50S ribosomal protein L24 | protein | 102 | 3% helix, 43% strand | P60624 |
| Y | 50S ribosomal protein L29 | protein | 63 | 57% helix, 0% strand | P0A7M6 |
| 0 | 50S ribosomal protein L32 | protein | 56 | 20% helix, 18% strand | P0A7N4 |
| 2 | 50S ribosomal protein L34 | protein | 46 | 52% helix, 0% strand | P0A7P5 |
| Z | 50S ribosomal protein L30 | protein | 58 | 33% helix, 26% strand | P0AG51 |
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 | 1101 | 0.87 | 0.89 | 85 | empty |
| 2 | 569 | 0.86 | 0.93 | 79 | empty |
| 3 | 623 | 0.85 | 0.91 | 72 | empty |
| 4 | 891 | 0.85 | 0.87 | 90 | empty |
| 5 | 657 | 0.84 | 0.89 | 78 | empty |
Interfaces
34 interfaces between chains.
- A–Q · 4243 Ų buried · 80 hydrogen bonds · protein-nucleic
- A–E · 4028 Ų buried · 76 hydrogen bonds · protein-nucleic
- A–C · 3895 Ų buried · 82 hydrogen bonds · protein-nucleic
- A–N · 3496 Ų buried · 54 hydrogen bonds · protein-nucleic
- A–D · 3201 Ų buried · 57 hydrogen bonds · protein-nucleic
Compared structures
- 6GC6 · 50S ribosomal subunit assembly intermediate state 2 · 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 P60422
- Every structure of UniProt P60438
- Every structure of UniProt P60723
- Every structure of UniProt P0AG55
- Every structure of UniProt P0AA10
- Every structure of UniProt P0ADY3
- Every structure of UniProt P02413
- Every structure of UniProt P0AG44
- Every structure of UniProt P0A7K6
- Every structure of UniProt P0A7L3
- Every structure of UniProt P0AG48
- Every structure of UniProt P61175
- Every structure of UniProt P0ADZ0
- Every structure of UniProt P60624
- Every structure of UniProt P0A7M6
- Every structure of UniProt P0A7N4
- Every structure of UniProt P0A7P5
- Every structure of UniProt P0AG51
- Elsewhere: RCSB PDB 6GC6 · PDBe 6GC6 · UniProt P60422 · UniProt P60438 · UniProt P60723 · UniProt P0AG55 · UniProt P0AA10 · UniProt P0ADY3 · UniProt P02413 · UniProt P0AG44 · UniProt P0A7K6 · UniProt P0A7L3 · UniProt P0AG48 · UniProt P61175 · UniProt P0ADZ0 · UniProt P60624 · UniProt P0A7M6 · UniProt P0A7N4 · UniProt P0A7P5 · UniProt P0AG51
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