MolNFT v1 · #151883 · protein + RNA
Tnac-stalled ribosome complex with the titin I27 domain folding close to the ribosomal exit tunnel
6I0Y · 50S ribosomal protein L24: “Tnac-stalled ribosome complex with the titin I27 domain folding close to the ribosomal exit tunnel”. Electron microscopy, 3 ligands (TRP, MG, ZN), 20 pockets (best druggability 0.87). MolNFT v1 #151883 on…
- PDB
- 6I0Y
- Type
- protein + RNA
- Length
- 6,599 residues
- Chains
- 36
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 50S ribosomal protein L24; 50S ribosomal protein L32; 50S ribosomal protein L33; 50S…
- EC
- 2.7.11.1
- UniProt
- P60624, P0A7N4, P0A7N9, P0A7P5, P0A7Q1, P0A7Q6, P0A7J3, P0A7K2, P0AD89, P68919, P60422, P60438, P60723, P62399, P0AG55, P0A7R1, P0A7J7, P0AA10, P0ADY3, P02413, P0ADY7, P0AG44, P0C018, P0A7K6, P0A7L3, P0AG48, P61175, P0ADZ0, P0A7L8, P0A7M2, P0A7M6, P0AG51, Q8WZ42
- Ligands
- TRP, MG, ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 36 distinct chains · 24% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| h | 50S ribosomal protein L24 | protein | 102 | 0% helix, 50% strand | P60624 |
| 0 | 50S ribosomal protein L32 | protein | 56 | 18% helix, 18% 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 |
| 3 | 50S ribosomal protein L35 | protein | 64 | 27% helix, 3% strand | P0A7Q1 |
| 4 | 50S ribosomal protein L36 | protein | 38 | 8% helix, 29% strand | P0A7Q6 |
| 5 | 50S ribosomal protein L10 | protein | 148 | 36% helix, 3% strand | P0A7J3 |
| 6 | 50S ribosomal protein L7/L12 | protein | 30 | 37% helix, 0% strand | P0A7K2 |
| 7 | Tryptophanase operon leader peptide | protein | 16 | 56% helix, 0% strand | P0AD89 |
| 8 | 50S ribosomal protein L25 | protein | 94 | 22% helix, 43% strand | P68919 |
| A | 23S ribosomal RNA | rna | 2854 | — | — |
| B | 5S ribosomal RNA | rna | 118 | — | — |
| C | 50S ribosomal protein L2 | protein | 271 | 8% helix, 20% strand | P60422 |
| D | 50S ribosomal protein L3 | protein | 209 | 7% helix, 25% strand | P60438 |
| E | 50S ribosomal protein L4 | protein | 201 | 31% helix, 4% strand | P60723 |
| F | 50S ribosomal protein L5 | protein | 177 | 36% helix, 16% strand | P62399 |
| G | 50S ribosomal protein L6 | protein | 175 | 18% helix, 23% strand | P0AG55 |
| H | 50S ribosomal protein L9 | protein | 50 | 28% helix, 10% strand | P0A7R1 |
| I | 50S ribosomal protein L11 | protein | 141 | 18% helix, 4% strand | P0A7J7 |
| J | 50S ribosomal protein L13 | protein | 142 | 32% helix, 14% strand | P0AA10 |
| K | 50S ribosomal protein L14 | protein | 122 | 9% helix, 35% strand | P0ADY3 |
| L | 50S ribosomal protein L15 | protein | 143 | 15% helix, 10% strand | P02413 |
| M | 50S ribosomal protein L16 | protein | 136 | 20% helix, 21% strand | P0ADY7 |
| N | 50S ribosomal protein L17 | protein | 120 | 48% helix, 13% strand | P0AG44 |
| O | 50S ribosomal protein L18 | protein | 116 | 41% helix, 16% strand | P0C018 |
| P | 50S ribosomal protein L19 | protein | 114 | 18% helix, 32% strand | P0A7K6 |
| Q | 50S ribosomal protein L20 | protein | 117 | 76% helix, 0% strand | P0A7L3 |
| R | 50S ribosomal protein L21 | protein | 103 | 0% helix, 54% strand | P0AG48 |
| S | 50S ribosomal protein L22 | protein | 110 | 29% helix, 34% strand | P61175 |
| T | 50S ribosomal protein L23 | protein | 93 | 19% helix, 18% strand | P0ADZ0 |
| V | Proline tRNA | rna | 77 | — | — |
| W | 50S ribosomal protein L27 | protein | 79 | 0% helix, 10% strand | P0A7L8 |
| X | 50S ribosomal protein L28 | protein | 77 | 22% helix, 21% strand | P0A7M2 |
| Y | 50S ribosomal protein L29 | protein | 63 | 67% helix, 0% strand | P0A7M6 |
| Z | 50S ribosomal protein L30 | protein | 58 | 38% helix, 17% strand | P0AG51 |
| z | Titin (EC 2.7.11.1) | protein | 89 | 0% helix, 37% strand | Q8WZ42 |
Ligands and binding sites
- TRP · Tryptophan · ligand · chains 7, A
- MG · Magnesium ion · metal · 143 copies · chains 4, A, E, L, C, Q, R, D, 3, T, J, B, 8
- ZN · Zinc ion · metal · chains 4
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 | 1113 | 0.87 | 0.89 | 100 | MG |
| 2 | 1063 | 0.86 | 0.88 | 100 | MG |
| 3 | 635 | 0.86 | 0.91 | 79 | MG |
| 4 | 1050 | 0.86 | 0.88 | 91 | empty |
| 5 | 702 | 0.86 | 0.91 | 75 | empty |
Interfaces
72 interfaces between chains.
- A–C · 7190 Ų buried · 212 hydrogen bonds · protein-nucleic
- A–D · 5015 Ų buried · 112 hydrogen bonds · protein-nucleic
- A–L · 4466 Ų buried · 126 hydrogen bonds · protein-nucleic
- A–E · 4227 Ų buried · 96 hydrogen bonds · protein-nucleic
- A–Q · 4136 Ų buried · 110 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 6I0Y · TnaC-stalled ribosome complex with the titin I27 domain folding close to the ribosomal… · the same entry in another collection · chain 8 against 8, 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 P60624
- Every structure of UniProt P0A7N4
- Every structure of UniProt P0A7N9
- Every structure of UniProt P0A7P5
- Every structure of UniProt P0A7Q1
- Every structure of UniProt P0A7Q6
- Every structure of UniProt P0A7J3
- Every structure of UniProt P0A7K2
- Every structure of UniProt P0AD89
- Every structure of UniProt P68919
- Every structure of UniProt P60422
- Every structure of UniProt P60438
- Every structure of UniProt P60723
- Every structure of UniProt P62399
- Every structure of UniProt P0AG55
- Every structure of UniProt P0A7R1
- Every structure of UniProt P0A7J7
- Every structure of UniProt P0AA10
- Every structure of UniProt P0ADY3
- Every structure of UniProt P02413
- Every structure of UniProt P0ADY7
- Every structure of UniProt P0AG44
- Every structure of UniProt P0C018
- 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 P0A7L8
- Every structure of UniProt P0A7M2
- Every structure of UniProt P0A7M6
- Every structure of UniProt P0AG51
- Every structure of UniProt Q8WZ42
- Elsewhere: RCSB PDB 6I0Y · PDBe 6I0Y · UniProt P60624 · UniProt P0A7N4 · UniProt P0A7N9 · UniProt P0A7P5 · UniProt P0A7Q1 · UniProt P0A7Q6 · UniProt P0A7J3 · UniProt P0A7K2 · UniProt P0AD89 · UniProt P68919 · UniProt P60422 · UniProt P60438 · UniProt P60723 · UniProt P62399 · UniProt P0AG55 · UniProt P0A7R1 · UniProt P0A7J7 · UniProt P0AA10 · UniProt P0ADY3 · UniProt P02413 · UniProt P0ADY7 · UniProt P0AG44 · UniProt P0C018 · UniProt P0A7K6 · UniProt P0A7L3 · UniProt P0AG48 · UniProt P61175 · UniProt P0ADZ0 · UniProt P0A7L8 · UniProt P0A7M2 · UniProt P0A7M6 · UniProt P0AG51 · UniProt Q8WZ42
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.