MolNFT v1 · #128955 · protein + RNA
Structure of the 50S large ribosomal subunit from mycobacterium smegmatis
5O60 · 50S ribosomal protein BL37: “Structure of the 50S large ribosomal subunit from mycobacterium smegmatis”. Electron microscopy, 3 ligands (PHE, MG, ZN), 20 pockets (best druggability 0.88). MolNFT v1 #128955 on GenesisL1: 3D…
- PDB
- 5O60
- Type
- protein + RNA
- Length
- 6,921 residues
- Chains
- 35
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 50S ribosomal protein BL37; 23S rRNA; 5S rRNA; 50S ribosomal protein L2; 50S ribosomal…
- UniProt
- A0QTP4, A0QSD4, A0QSD1, A0QSD2, A0QSG1, A0QSG4, A0R7F6, A0QS62, A0QS45, A0QSP8, A0QSF9, A0QSG8, A0QSD8, A0QSL9, A0QSG5, A0QV42, A0QYU6, A0R151, A0QSD6, A0QSD3, A0QSG0, A0R3D2, A0R150, A0QV03, A0QSD9, A0QSG7, A0R3I9, A0QS39, A0R7K0, A0QYU7, A0QSL4, A0R215
- Ligands
- PHE, MG, ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 35 distinct chains · 27% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 3 | 50S ribosomal protein BL37 | protein | 23 | 39% helix, 0% strand | A0QTP4 |
| A | 23S rRNA | rna | 3119 | — | — |
| B | 5S rRNA | rna | 118 | — | — |
| C | 50S ribosomal protein L2 | protein | 275 | 7% helix, 28% strand | A0QSD4 |
| D | 50S ribosomal protein L3 | protein | 214 | 8% helix, 37% strand | A0QSD1 |
| E | 50S ribosomal protein L4 | protein | 209 | 36% helix, 12% strand | A0QSD2 |
| F | 50S ribosomal protein L5 | protein | 182 | 39% helix, 21% strand | A0QSG1 |
| G | 50S ribosomal protein L6 | protein | 176 | 19% helix, 37% strand | A0QSG4 |
| H | 50S ribosomal protein L9 | protein | 151 | 33% helix, 25% strand | A0R7F6 |
| I | 50S ribosomal protein L10 | protein | 126 | 45% helix, 20% strand | A0QS62 |
| J | 50S ribosomal protein L11 | protein | 133 | 41% helix, 16% strand | A0QS45 |
| K | 50S ribosomal protein L13 | protein | 146 | 34% helix, 18% strand | A0QSP8 |
| L | 50S ribosomal protein L14 | protein | 122 | 8% helix, 39% strand | A0QSF9 |
| M | 50S ribosomal protein L15 | protein | 145 | 23% helix, 14% strand | A0QSG8 |
| N | 50S ribosomal protein L16 | protein | 136 | 20% helix, 27% strand | A0QSD8 |
| O | 50S ribosomal protein L17 | protein | 118 | 53% helix, 17% strand | A0QSL9 |
| P | 50S ribosomal protein L18 | protein | 126 | 40% helix, 20% strand | A0QSG5 |
| Q | 50S ribosomal protein L19 | protein | 113 | 16% helix, 47% strand | A0QV42 |
| R | 50S ribosomal protein L20 | protein | 124 | 73% helix, 0% strand | A0QYU6 |
| S | 50S ribosomal protein L21 | protein | 100 | 6% helix, 62% strand | A0R151 |
| T | 50S ribosomal protein L22 | protein | 114 | 36% helix, 40% strand | A0QSD6 |
| U | 50S ribosomal protein L23 | protein | 97 | 23% helix, 32% strand | A0QSD3 |
| V | 50S ribosomal protein L24 | protein | 97 | 3% helix, 53% strand | A0QSG0 |
| W | 50S ribosomal protein L25 | protein | 192 | 14% helix, 47% strand | A0R3D2 |
| X | 50S ribosomal protein L27 | protein | 79 | 0% helix, 39% strand | A0R150 |
| Y | 50S ribosomal protein L28 | protein | 63 | 10% helix, 41% strand | A0QV03 |
| Z | 50S ribosomal protein L29 | protein | 64 | 78% helix, 0% strand | A0QSD9 |
| a | 50S ribosomal protein L30 | protein | 59 | 34% helix, 29% strand | A0QSG7 |
| b | 50S ribosomal protein L32 | protein | 54 | 30% helix, 22% strand | A0R3I9 |
| c | 50S ribosomal protein L33 1 | protein | 49 | 0% helix, 51% strand | A0QS39 |
| d | 50S ribosomal protein L34 | protein | 46 | 57% helix, 0% strand | A0R7K0 |
| e | 50S ribosomal protein L35 | protein | 63 | 37% helix, 14% strand | A0QYU7 |
| f | 50S ribosomal protein L36 | protein | 37 | 8% helix, 43% strand | A0QSL4 |
| g | 50S ribosomal protein L31 | protein | 48 | 8% helix, 35% strand | A0R215 |
| 2 | TRNA cca-end acetylated (phe) | rna | 3 | — | — |
Ligands and binding sites
- PHE · Phenylalanine · ligand · chains A, 2
- MG · Magnesium ion · metal · 408 copies · chains A, C, M, E, b, U, D, d, S, K, O, N, H, e, Q, V, X, c, a, R, Y, 3, B, F, T, 2
- ZN · Zinc ion · metal · 4 copies · chains Y, c, f, g
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 | 966 | 0.88 | 0.90 | 113 | MG |
| 2 | 993 | 0.87 | 0.89 | 100 | MG |
| 3 | 661 | 0.87 | 0.93 | 93 | MG |
| 4 | 1018 | 0.87 | 0.89 | 92 | MG |
| 5 | 681 | 0.87 | 0.92 | 67 | MG |
Interfaces
66 interfaces between chains.
- A–C · 7058 Ų buried · 153 hydrogen bonds · protein-nucleic
- A–D · 4875 Ų buried · 94 hydrogen bonds · protein-nucleic
- A–M · 4542 Ų buried · 96 hydrogen bonds · protein-nucleic
- A–R · 4381 Ų buried · 124 hydrogen bonds · protein-nucleic
- A–E · 4319 Ų buried · 90 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- A0QSD4 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L2 (A0QSD4) · a predicted model of the same protein · chain C against A, TM-score 0.99
- A0QSD6 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L22 (A0QSD6) · a predicted model of the same protein · chain T against A, TM-score 0.99
- A0QSD1 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L3 (A0QSD1) · a predicted model of the same protein · chain D against A, TM-score 0.99
- A0QSL9 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L17 (A0QSL9) · a predicted model of the same protein · chain O against A, TM-score 0.98
- A0QSF9 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L14 (A0QSF9) · a predicted model of the same protein · chain L against A, TM-score 0.98
- A0QSD8 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L16 (A0QSD8) · a predicted model of the same protein · chain N against A, TM-score 0.98
- A0QSG1 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L5 (A0QSG1) · a predicted model of the same protein · chain F against A, TM-score 0.98
- A0QSD2 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L4 (A0QSD2) · a predicted model of the same protein · chain E against A, TM-score 0.97
- A0R151 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L21 (A0R151) · a predicted model of the same protein · chain S against A, TM-score 0.97
- A0QSG7 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L30 (A0QSG7) · a predicted model of the same protein · chain a against A, TM-score 0.97
- A0QV42 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L19 (A0QV42) · a predicted model of the same protein · chain Q against A, TM-score 0.96
- A0R150 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L27 (A0R150) · a predicted model of the same protein · chain X against A, TM-score 0.96
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 A0QTP4
- Every structure of UniProt A0QSD4
- Every structure of UniProt A0QSD1
- Every structure of UniProt A0QSD2
- Every structure of UniProt A0QSG1
- Every structure of UniProt A0QSG4
- Every structure of UniProt A0R7F6
- Every structure of UniProt A0QS62
- Every structure of UniProt A0QS45
- Every structure of UniProt A0QSP8
- Every structure of UniProt A0QSF9
- Every structure of UniProt A0QSG8
- Every structure of UniProt A0QSD8
- Every structure of UniProt A0QSL9
- Every structure of UniProt A0QSG5
- Every structure of UniProt A0QV42
- Every structure of UniProt A0QYU6
- Every structure of UniProt A0R151
- Every structure of UniProt A0QSD6
- Every structure of UniProt A0QSD3
- Every structure of UniProt A0QSG0
- Every structure of UniProt A0R3D2
- Every structure of UniProt A0R150
- Every structure of UniProt A0QV03
- Every structure of UniProt A0QSD9
- Every structure of UniProt A0QSG7
- Every structure of UniProt A0R3I9
- Every structure of UniProt A0QS39
- Every structure of UniProt A0R7K0
- Every structure of UniProt A0QYU7
- Every structure of UniProt A0QSL4
- Every structure of UniProt A0R215
- Elsewhere: RCSB PDB 5O60 · PDBe 5O60 · UniProt A0QTP4 · UniProt A0QSD4 · UniProt A0QSD1 · UniProt A0QSD2 · UniProt A0QSG1 · UniProt A0QSG4 · UniProt A0R7F6 · UniProt A0QS62 · UniProt A0QS45 · UniProt A0QSP8 · UniProt A0QSF9 · UniProt A0QSG8 · UniProt A0QSD8 · UniProt A0QSL9 · UniProt A0QSG5 · UniProt A0QV42 · UniProt A0QYU6 · UniProt A0R151 · UniProt A0QSD6 · UniProt A0QSD3 · UniProt A0QSG0 · UniProt A0R3D2 · UniProt A0R150 · UniProt A0QV03 · UniProt A0QSD9 · UniProt A0QSG7 · UniProt A0R3I9 · UniProt A0QS39 · UniProt A0R7K0 · UniProt A0QYU7 · UniProt A0QSL4 · UniProt A0R215
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.