Research workbench
RNase M5 bound to 50S ribosome with precursor 5S rRNA
Analyse RNase M5 bound to 50S ribosome with precursor 5S rRNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TPQ
- Type
- protein + RNA
- Length
- 6,393 residues
- Chains
- 31
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease M5; Pre-5S rRNA; 50S ribosomal protein L10; Pre-23S rRNA; 50S ribosomal…
- EC
- 3.1.26.8
- UniProt
- A0A087LGV4, P42923, P42919, P42920, P42921, P12877, P46898, P70974, P12875, P19946, P14577, P20277, P46899, O31742, P55873, P26908, P42060, P42924, P0CI78, P05657, O34687, P56849, P05647, P55874, P20278, P37807, P12873, P19947
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 31 distinct chains · 26% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Ribonuclease M5 (EC 3.1.26.8) | protein | 183 | 49% helix, 7% strand | A0A087LGV4 |
| V | Pre-5S rRNA | rna | 123 | — | — |
| A | Ribonuclease M5 (EC 3.1.26.8) | protein | 69 | 64% helix, 0% strand | A0A087LGV4 |
| b | 50S ribosomal protein L10 | protein | 123 | 37% helix, 5% strand | P42923 |
| U | Pre-23S rRNA | rna | 2924 | — | — |
| W | 50S ribosomal protein L2 | protein | 275 | 8% helix, 24% strand | P42919 |
| X | 50S ribosomal protein L3 | protein | 207 | 9% helix, 38% strand | P42920 |
| Y | 50S ribosomal protein L4 | protein | 205 | 32% helix, 12% strand | P42921 |
| Z | 50S ribosomal protein L5 | protein | 178 | 30% helix, 14% strand | P12877 |
| a | 50S ribosomal protein L6 | protein | 175 | 23% helix, 29% strand | P46898 |
| c | 50S ribosomal protein L13 | protein | 142 | 26% helix, 18% strand | P70974 |
| d | 50S ribosomal protein L14 | protein | 122 | 5% helix, 39% strand | P12875 |
| e | 50S ribosomal protein L15 | protein | 146 | 17% helix, 10% strand | P19946 |
| f | 50S ribosomal protein L16 | protein | 138 | 19% helix, 25% strand | P14577 |
| g | 50S ribosomal protein L17 | protein | 119 | 51% helix, 21% strand | P20277 |
| h | 50S ribosomal protein L18 | protein | 120 | 35% helix, 19% strand | P46899 |
| i | 50S ribosomal protein L19 | protein | 114 | 13% helix, 39% strand | O31742 |
| j | 50S ribosomal protein L20 | protein | 117 | 74% helix, 0% strand | P55873 |
| k | 50S ribosomal protein L21 | protein | 101 | 0% helix, 47% strand | P26908 |
| l | 50S ribosomal protein L22 | protein | 109 | 38% helix, 32% strand | P42060 |
| m | 50S ribosomal protein L23 | protein | 93 | 25% helix, 30% strand | P42924 |
| n | 50S ribosomal protein L24 | protein | 101 | 3% helix, 37% strand | P0CI78 |
| o | 50S ribosomal protein L27 | protein | 82 | 0% helix, 38% strand | P05657 |
| p | 50S ribosomal protein L32 | protein | 54 | 19% helix, 9% strand | O34687 |
| q | 50S ribosomal protein L33 1 | protein | 48 | 0% helix, 56% strand | P56849 |
| r | 50S ribosomal protein L34 | protein | 44 | 57% helix, 0% strand | P05647 |
| s | 50S ribosomal protein L35 | protein | 64 | 31% helix, 0% strand | P55874 |
| t | 50S ribosomal protein L36 | protein | 36 | 8% helix, 42% strand | P20278 |
| u | 50S ribosomal protein L28 | protein | 58 | 5% helix, 38% strand | P37807 |
| v | 50S ribosomal protein L29 | protein | 65 | 80% helix, 0% strand | P12873 |
| w | 50S ribosomal protein L30 | protein | 58 | 31% helix, 28% strand | P19947 |
Ligands and binding sites
- MG · Magnesium ion · metal · 219 copies · chains V, U, Y, e, k, W, c, m, t, o, u
- ZN · Zinc ion · metal · 3 copies · chains p, q, t
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 | 947 | 0.89 | 0.91 | 102 | MG |
| 2 | 1093 | 0.88 | 0.91 | 88 | MG |
| 3 | 1041 | 0.88 | 0.90 | 104 | MG |
| 4 | 697 | 0.88 | 0.93 | 84 | MG |
| 5 | 944 | 0.86 | 0.89 | 95 | MG |
Interfaces
57 interfaces between chains.
- U–W · 7135 Ų buried · 148 hydrogen bonds · protein-nucleic
- U–X · 4935 Ų buried · 84 hydrogen bonds · protein-nucleic
- U–e · 4220 Ų buried · 87 hydrogen bonds · protein-nucleic
- U–Y · 4172 Ų buried · 66 hydrogen bonds · protein-nucleic
- U–j · 3903 Ų buried · 62 hydrogen bonds · protein-nucleic
Compared structures
- 6TPQ · RNase M5 bound to 50S ribosome with precursor 5S rRNA · the same entry in another collection · chain c against c, 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 A0A087LGV4
- Every structure of UniProt P42923
- Every structure of UniProt P42919
- Every structure of UniProt P42920
- Every structure of UniProt P42921
- Every structure of UniProt P12877
- Every structure of UniProt P46898
- Every structure of UniProt P70974
- Every structure of UniProt P12875
- Every structure of UniProt P19946
- Every structure of UniProt P14577
- Every structure of UniProt P20277
- Every structure of UniProt P46899
- Every structure of UniProt O31742
- Every structure of UniProt P55873
- Every structure of UniProt P26908
- Every structure of UniProt P42060
- Every structure of UniProt P42924
- Every structure of UniProt P0CI78
- Every structure of UniProt P05657
- Every structure of UniProt O34687
- Every structure of UniProt P56849
- Every structure of UniProt P05647
- Every structure of UniProt P55874
- Every structure of UniProt P20278
- Every structure of UniProt P37807
- Every structure of UniProt P12873
- Every structure of UniProt P19947
- Elsewhere: RCSB PDB 6TPQ · PDBe 6TPQ · UniProt A0A087LGV4 · UniProt P42923 · UniProt P42919 · UniProt P42920 · UniProt P42921 · UniProt P12877 · UniProt P46898 · UniProt P70974 · UniProt P12875 · UniProt P19946 · UniProt P14577 · UniProt P20277 · UniProt P46899 · UniProt O31742 · UniProt P55873 · UniProt P26908 · UniProt P42060 · UniProt P42924 · UniProt P0CI78 · UniProt P05657 · UniProt O34687 · UniProt P56849 · UniProt P05647 · UniProt P55874 · UniProt P20278 · UniProt P37807 · UniProt P12873 · UniProt P19947
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