MolNFT v1 · #149842 · protein + RNA
50S ribosomal subunit assembly intermediate state 3
6GC4 · 50S ribosomal protein L25: “50S ribosomal subunit assembly intermediate state 3”. Electron microscopy, 20 pockets (best druggability 0.88). MolNFT v1 #149842 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6GC4
- Type
- protein + RNA
- Length
- 5,541 residues
- Chains
- 26
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 50S ribosomal protein L25; 23S ribosomal RNA; 50S ribosomal protein L2; 50S ribosomal…
- UniProt
- P68919, P60422, P60438, P60723, P0AG55, P0AA10, P0ADY3, P02413, P0AG44, P0A7K6, P0A7L3, P0AG48, P61175, P0ADZ0, P60624, P0A7M2, P0A7M6, P0A7N4, P0A7P5, P0C018, P62399, P0AG51, P0A7R1, P0A7L8
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 26 distinct chains · 23% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| V | 50S ribosomal protein L25 | protein | 94 | 16% helix, 45% strand | P68919 |
| A | 23S ribosomal RNA | rna | 2586 | — | — |
| C | 50S ribosomal protein L2 | protein | 271 | 6% helix, 27% strand | P60422 |
| D | 50S ribosomal protein L3 | protein | 209 | 7% helix, 34% strand | P60438 |
| E | 50S ribosomal protein L4 | protein | 201 | 34% helix, 10% strand | P60723 |
| G | 50S ribosomal protein L6 | protein | 176 | 16% helix, 28% strand | P0AG55 |
| J | 50S ribosomal protein L13 | protein | 142 | 27% helix, 18% strand | P0AA10 |
| K | 50S ribosomal protein L14 | protein | 122 | 3% helix, 34% strand | P0ADY3 |
| L | 50S ribosomal protein L15 | protein | 143 | 8% helix, 8% strand | P02413 |
| N | 50S ribosomal protein L17 | protein | 120 | 43% helix, 17% strand | P0AG44 |
| P | 50S ribosomal protein L19 | protein | 114 | 15% helix, 44% strand | P0A7K6 |
| Q | 50S ribosomal protein L20 | protein | 117 | 76% helix, 0% strand | P0A7L3 |
| R | 50S ribosomal protein L21 | protein | 103 | 0% helix, 57% strand | P0AG48 |
| S | 50S ribosomal protein L22 | protein | 110 | 39% helix, 35% strand | P61175 |
| T | 50S ribosomal protein L23 | protein | 93 | 26% helix, 27% strand | P0ADZ0 |
| U | 50S ribosomal protein L24 | protein | 102 | 0% helix, 41% strand | P60624 |
| X | 50S ribosomal protein L28 | protein | 77 | 22% helix, 31% strand | P0A7M2 |
| Y | 50S ribosomal protein L29 | protein | 63 | 59% helix, 0% strand | P0A7M6 |
| 0 | 50S ribosomal protein L32 | protein | 56 | 13% helix, 18% strand | P0A7N4 |
| 2 | 50S ribosomal protein L34 | protein | 46 | 57% helix, 0% strand | P0A7P5 |
| O | 50S ribosomal protein L18 | protein | 116 | 40% helix, 16% strand | P0C018 |
| F | 50S ribosomal protein L5 | protein | 177 | 35% helix, 15% strand | P62399 |
| B | 5S ribosomal RNA | rna | 119 | — | — |
| Z | 50S ribosomal protein L30 | protein | 58 | 33% helix, 26% strand | P0AG51 |
| H | 50S ribosomal protein L9 | protein | 50 | 30% helix, 10% strand | P0A7R1 |
| W | 50S ribosomal protein L27 | protein | 76 | 0% helix, 37% strand | P0A7L8 |
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 | 1121 | 0.88 | 0.90 | 107 | empty |
| 2 | 681 | 0.88 | 0.93 | 98 | empty |
| 3 | 824 | 0.87 | 0.90 | 89 | empty |
| 4 | 1061 | 0.86 | 0.87 | 93 | empty |
| 5 | 838 | 0.86 | 0.89 | 78 | empty |
Interfaces
47 interfaces between chains.
- A–C · 6471 Ų buried · 129 hydrogen bonds · protein-nucleic
- A–D · 4485 Ų buried · 79 hydrogen bonds · protein-nucleic
- A–Q · 4263 Ų buried · 88 hydrogen bonds · protein-nucleic
- A–L · 4182 Ų buried · 76 hydrogen bonds · protein-nucleic
- A–E · 4092 Ų buried · 70 hydrogen bonds · protein-nucleic
Compared structures
- 6GC4 · 50S ribosomal subunit assembly intermediate state 3 · the same entry in another collection · chain L against L, 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 P68919
- 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 P0A7M2
- Every structure of UniProt P0A7M6
- Every structure of UniProt P0A7N4
- Every structure of UniProt P0A7P5
- Every structure of UniProt P0C018
- Every structure of UniProt P62399
- Every structure of UniProt P0AG51
- Every structure of UniProt P0A7R1
- Every structure of UniProt P0A7L8
- Elsewhere: RCSB PDB 6GC4 · PDBe 6GC4 · UniProt P68919 · 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 P0A7M2 · UniProt P0A7M6 · UniProt P0A7N4 · UniProt P0A7P5 · UniProt P0C018 · UniProt P62399 · UniProt P0AG51 · UniProt P0A7R1 · UniProt P0A7L8
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