MolNFT v1 · #120482 · protein + RNA
Structure of the large subunit of the chloro-ribosome
5H1S · 23S rRNA: “Structure of the large subunit of the chloro-ribosome”. Electron microscopy, 20 pockets (best druggability 0.90). MolNFT v1 #120482 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5H1S
- Type
- protein + RNA
- Length
- 6,294 residues
- Chains
- 32
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S rRNA; Spinach chloroplast 4.5S rRNA; 5S rRNA; 50S ribosomal protein L13…
- UniProt
- P12629, P09596, A0A0K9QHT0, P17353, A0A0K9RLJ4, A0A0K9QQ60, P82413, P28803, P24613, P09594, Q9LWB5, P27683, A0A0K9R4I2, A0A0K9RD02, A0A0K9R7W8, P06509, P28804, P28805, P82244, P23326, P12230, A0A0K9QEC7, O49937, P82192, A0A0K9R4N9, A0A0K9RQ91, P27684, A0A0K9R0R6, P82411
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 32 distinct chains · 24% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 23S rRNA | rna | 2799 | — | — |
| C | Spinach chloroplast 4.5S rRNA | rna | 102 | — | — |
| B | 5S rRNA | rna | 117 | — | — |
| L | 50S ribosomal protein L13, chloroplastic | protein | 147 | 27% helix, 13% strand | P12629 |
| M | 50S ribosomal protein L14, chloroplastic | protein | 121 | 7% helix, 38% strand | P09596 |
| N | 50S ribosomal protein L15 | protein | 177 | 23% helix, 2% strand | A0A0K9QHT0 |
| O | 50S ribosomal protein L16, chloroplastic | protein | 134 | 21% helix, 19% strand | P17353 |
| P | 50S ribosomal protein L17 | protein | 116 | 50% helix, 16% strand | A0A0K9RLJ4 |
| Q | 50S ribosomal protein L18 | protein | 120 | 34% helix, 23% strand | A0A0K9QQ60 |
| R | 50S ribosomal protein L19, chloroplastic | protein | 118 | 18% helix, 35% strand | P82413 |
| S | 50S ribosomal protein L20, chloroplastic | protein | 115 | 68% helix, 0% strand | P28803 |
| T | 50S ribosomal protein L21, chloroplastic | protein | 147 | 4% helix, 30% strand | P24613 |
| U | 50S ribosomal protein L22, chloroplastic | protein | 144 | 29% helix, 22% strand | P09594 |
| V | 50S ribosomal protein L23, chloroplastic | protein | 92 | 27% helix, 27% strand | Q9LWB5 |
| W | 50S ribosomal protein L24, chloroplastic | protein | 124 | 5% helix, 24% strand | P27683 |
| X | 50S ribosomal protein L27 | protein | 100 | 16% helix, 20% strand | A0A0K9R4I2 |
| Y | 50S ribosomal protein L28 | protein | 74 | 27% helix, 27% strand | A0A0K9RD02 |
| Z | 50S ribosomal protein L29 | protein | 90 | 67% helix, 0% strand | A0A0K9R7W8 |
| E | 50S ribosomal protein L2, chloroplastic | protein | 247 | 4% helix, 21% strand | P06509 |
| b | 50S ribosomal protein L32, chloroplastic | protein | 46 | 63% helix, 2% strand | P28804 |
| c | 50S ribosomal protein L33, chloroplastic | protein | 51 | 0% helix, 20% strand | P28805 |
| d | 50S ribosomal protein L34, chloroplastic | protein | 57 | 47% helix, 0% strand | P82244 |
| e | 50S ribosomal protein L35, chloroplastic | protein | 69 | 19% helix, 7% strand | P23326 |
| f | 50S ribosomal protein L36, chloroplastic | protein | 37 | 8% helix, 32% strand | P12230 |
| F | 50S ribosomal protein L3 | protein | 212 | 6% helix, 33% strand | A0A0K9QEC7 |
| G | 50S ribosomal protein L4, chloroplastic | protein | 210 | 25% helix, 1% strand | O49937 |
| H | 50S ribosomal protein L5, chloroplastic | protein | 175 | 30% helix, 9% strand | P82192 |
| I | 50S ribosomal protein L6 | protein | 173 | 20% helix, 30% strand | A0A0K9R4N9 |
| J | 50S ribosomal protein L9 | protein | 53 | 23% helix, 8% strand | A0A0K9RQ91 |
| g | 50S ribosomal protein 5 alpha, chloroplastic | protein | 43 | 79% helix, 0% strand | P27684 |
| a | 50S ribosomal protein L31 | protein | 38 | 0% helix, 11% strand | A0A0K9R0R6 |
| h | 50S ribosomal protein 6, chloroplastic | protein | 46 | 22% helix, 0% strand | P82411 |
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 | 992 | 0.90 | 0.92 | 104 | empty |
| 2 | 801 | 0.88 | 0.92 | 87 | empty |
| 3 | 881 | 0.87 | 0.90 | 90 | empty |
| 4 | 924 | 0.87 | 0.89 | 95 | empty |
| 5 | 842 | 0.86 | 0.90 | 90 | empty |
Interfaces
68 interfaces between chains.
- A–E · 6621 Ų buried · 136 hydrogen bonds · protein-nucleic
- A–N · 5618 Ų buried · 140 hydrogen bonds · protein-nucleic
- A–F · 4466 Ų buried · 79 hydrogen bonds · protein-nucleic
- A–G · 4406 Ų buried · 85 hydrogen bonds · protein-nucleic
- A–S · 4096 Ų buried · 101 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5H1S · Structure of the large subunit of the chloro-ribosome · the same entry in another collection · chain S against S, 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 P12629
- Every structure of UniProt P09596
- Every structure of UniProt A0A0K9QHT0
- Every structure of UniProt P17353
- Every structure of UniProt A0A0K9RLJ4
- Every structure of UniProt A0A0K9QQ60
- Every structure of UniProt P82413
- Every structure of UniProt P28803
- Every structure of UniProt P24613
- Every structure of UniProt P09594
- Every structure of UniProt Q9LWB5
- Every structure of UniProt P27683
- Every structure of UniProt A0A0K9R4I2
- Every structure of UniProt A0A0K9RD02
- Every structure of UniProt A0A0K9R7W8
- Every structure of UniProt P06509
- Every structure of UniProt P28804
- Every structure of UniProt P28805
- Every structure of UniProt P82244
- Every structure of UniProt P23326
- Every structure of UniProt P12230
- Every structure of UniProt A0A0K9QEC7
- Every structure of UniProt O49937
- Every structure of UniProt P82192
- Every structure of UniProt A0A0K9R4N9
- Every structure of UniProt A0A0K9RQ91
- Every structure of UniProt P27684
- Every structure of UniProt A0A0K9R0R6
- Every structure of UniProt P82411
- Elsewhere: RCSB PDB 5H1S · PDBe 5H1S · UniProt P12629 · UniProt P09596 · UniProt A0A0K9QHT0 · UniProt P17353 · UniProt A0A0K9RLJ4 · UniProt A0A0K9QQ60 · UniProt P82413 · UniProt P28803 · UniProt P24613 · UniProt P09594 · UniProt Q9LWB5 · UniProt P27683 · UniProt A0A0K9R4I2 · UniProt A0A0K9RD02 · UniProt A0A0K9R7W8 · UniProt P06509 · UniProt P28804 · UniProt P28805 · UniProt P82244 · UniProt P23326 · UniProt P12230 · UniProt A0A0K9QEC7 · UniProt O49937 · UniProt P82192 · UniProt A0A0K9R4N9 · UniProt A0A0K9RQ91 · UniProt P27684 · UniProt A0A0K9R0R6 · UniProt P82411
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