MolNFT v1 · #174104 · protein + RNA
Pre-50S-obge particle
7BL5 · 50S ribosomal protein L2: “Pre-50S-obge particle”. Electron microscopy, 3 ligands (GDP, MG, ZN), 20 pockets (best druggability 0.88). MolNFT v1 #174104 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7BL5
- Type
- protein + RNA
- Length
- 7,380 residues
- Chains
- 35
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 50S ribosomal protein L2; 50S ribosomal protein L3; 50S ribosomal protein L4; 50S…
- EC
- 5.4.99.23, 3.6.5.-
- UniProt
- P60422, P60438, P60723, P0AG55, P0AA10, P02413, P0AG44, P0C018, P0A7L3, P0AG48, P61175, P0ADZ0, P60624, P68919, P0A7L8, P0A7M2, P0A7M6, P0AG51, P0A7N4, P0A7N9, P0A7P5, P0A7J7, P0ADY3, P0A7K6, P0AAT6, P33643, P0A8X0, P42641, P0ADY7, P0A7R1, P0A7J3, P62399, P0A7M9
- Ligands
- GDP, MG, ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 35 distinct chains · 25% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 50S ribosomal protein L2 | protein | 271 | 4% helix, 27% strand | P60422 |
| D | 50S ribosomal protein L3 | protein | 209 | 9% helix, 36% strand | P60438 |
| E | 50S ribosomal protein L4 | protein | 201 | 31% helix, 11% strand | P60723 |
| G | 50S ribosomal protein L6 | protein | 171 | 19% helix, 30% strand | P0AG55 |
| J | 50S ribosomal protein L13 | protein | 142 | 32% helix, 18% strand | P0AA10 |
| L | 50S ribosomal protein L15 | protein | 143 | 11% helix, 10% strand | P02413 |
| N | 50S ribosomal protein L17 | protein | 120 | 44% helix, 17% strand | P0AG44 |
| O | 50S ribosomal protein L18 | protein | 116 | 41% helix, 10% strand | P0C018 |
| Q | 50S ribosomal protein L20 | protein | 117 | 78% helix, 0% strand | P0A7L3 |
| R | 50S ribosomal protein L21 | protein | 103 | 0% helix, 57% strand | P0AG48 |
| S | 50S ribosomal protein L22 | protein | 110 | 35% helix, 35% strand | P61175 |
| T | 50S ribosomal protein L23 | protein | 93 | 25% helix, 31% strand | P0ADZ0 |
| U | 50S ribosomal protein L24 | protein | 102 | 3% helix, 43% strand | P60624 |
| V | 50S ribosomal protein L25 | protein | 94 | 20% helix, 46% strand | P68919 |
| W | 50S ribosomal protein L27 | protein | 76 | 0% helix, 39% strand | P0A7L8 |
| X | 50S ribosomal protein L28 | protein | 77 | 27% helix, 31% strand | P0A7M2 |
| Y | 50S ribosomal protein L29 | protein | 63 | 65% helix, 0% strand | P0A7M6 |
| Z | 50S ribosomal protein L30 | protein | 58 | 33% helix, 26% strand | P0AG51 |
| 0 | 50S ribosomal protein L32 | protein | 56 | 18% helix, 16% strand | P0A7N4 |
| 1 | 50S ribosomal protein L33 | protein | 50 | 0% helix, 48% strand | P0A7N9 |
| 2 | 50S ribosomal protein L34 | protein | 46 | 54% helix, 0% strand | P0A7P5 |
| B | 5S ribosomal RNA | rna | 119 | — | — |
| I | 50S ribosomal protein L11 | protein | 141 | 19% helix, 6% strand | P0A7J7 |
| K | 50S ribosomal protein L14 | protein | 122 | 7% helix, 37% strand | P0ADY3 |
| P | 50S ribosomal protein L19 | protein | 113 | 12% helix, 45% strand | P0A7K6 |
| 6 | Ribosomal silencing factor rsfs | protein | 102 | 35% helix, 25% strand | P0AAT6 |
| 7 | Ribosomal large subunit pseudouridine synthase D (EC 5.4.99.23) | protein | 317 | 25% helix, 25% strand | P33643 |
| 8 | UPF0307 protein yjga | protein | 157 | 73% helix, 0% strand | P0A8X0 |
| 9 | GTPase OBGE/CGTA (EC 3.6.5.-) | protein | 338 | 17% helix, 22% strand | P42641 |
| M | 50S ribosomal protein L16 | protein | 136 | 19% helix, 28% strand | P0ADY7 |
| A | 23S ribosomal RNA | rna | 2913 | — | — |
| H | 50S ribosomal protein L9 | protein | 149 | 36% helix, 20% strand | P0A7R1 |
| e | 50S ribosomal protein L10 | protein | 131 | 34% helix, 2% strand | P0A7J3 |
| F | 50S ribosomal protein L5 | protein | 177 | 34% helix, 20% strand | P62399 |
| b | 50S ribosomal protein L31 | protein | 47 | 0% helix, 21% strand | P0A7M9 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains 9
- MG · Magnesium ion · metal · 2 copies · chains 9
- ZN · Zinc ion · metal · chains b
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 710 | 0.88 | 0.92 | 75 | empty |
| 2 | 623 | 0.87 | 0.93 | 55 | empty |
| 3 | 703 | 0.86 | 0.91 | 74 | empty |
| 4 | 1054 | 0.86 | 0.87 | 73 | empty |
| 5 | 931 | 0.84 | 0.87 | 73 | MG |
Interfaces
71 interfaces between chains.
- C–A · 6998 Ų buried · 182 hydrogen bonds · protein-nucleic
- D–A · 5201 Ų buried · 113 hydrogen bonds · protein-nucleic
- L–A · 4586 Ų buried · 93 hydrogen bonds · protein-nucleic
- Q–A · 4231 Ų buried · 93 hydrogen bonds · protein-nucleic
- E–A · 4209 Ų buried · 89 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7BL5 · pre-50S-ObgE particle · 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 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 P02413
- Every structure of UniProt P0AG44
- Every structure of UniProt P0C018
- 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 P68919
- Every structure of UniProt P0A7L8
- Every structure of UniProt P0A7M2
- Every structure of UniProt P0A7M6
- Every structure of UniProt P0AG51
- Every structure of UniProt P0A7N4
- Every structure of UniProt P0A7N9
- Every structure of UniProt P0A7P5
- Every structure of UniProt P0A7J7
- Every structure of UniProt P0ADY3
- Every structure of UniProt P0A7K6
- Every structure of UniProt P0AAT6
- Every structure of UniProt P33643
- Every structure of UniProt P0A8X0
- Every structure of UniProt P42641
- Every structure of UniProt P0ADY7
- Every structure of UniProt P0A7R1
- Every structure of UniProt P0A7J3
- Every structure of UniProt P62399
- Every structure of UniProt P0A7M9
- Elsewhere: RCSB PDB 7BL5 · PDBe 7BL5 · UniProt P60422 · UniProt P60438 · UniProt P60723 · UniProt P0AG55 · UniProt P0AA10 · UniProt P02413 · UniProt P0AG44 · UniProt P0C018 · UniProt P0A7L3 · UniProt P0AG48 · UniProt P61175 · UniProt P0ADZ0 · UniProt P60624 · UniProt P68919 · UniProt P0A7L8 · UniProt P0A7M2 · UniProt P0A7M6 · UniProt P0AG51 · UniProt P0A7N4 · UniProt P0A7N9 · UniProt P0A7P5 · UniProt P0A7J7 · UniProt P0ADY3 · UniProt P0A7K6 · UniProt P0AAT6 · UniProt P33643 · UniProt P0A8X0 · UniProt P42641 · UniProt P0ADY7 · UniProt P0A7R1 · UniProt P0A7J3 · UniProt P62399 · UniProt P0A7M9
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