MolNFT v2 · #158953 · protein + RNA
Conformational switches control early maturation of the eukaryotic small ribosomal subunit
6ND4 · 5'ETS rRNA: “Conformational switches control early maturation of the eukaryotic small ribosomal subunit”. Electron microscopy at 4.3, 20 pockets (best druggability 0.85). MolNFT v2 #158953 on GenesisL1: 3D structure, binding sites…
- PDB
- 6ND4
- Type
- protein + RNA
- Length
- 11,082 residues
- Chains
- 30
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.3
- Source
- Saccharomyces cerevisiae BY4741
- Molecule
- 5'ETS rRNA; 18S rRNA 5' domain start; U3 snoRNA; Utp17; Utp8; Utp15; Utp9; Utp5; Utp10…
- EC
- 2.1.1.-
- UniProt
- Q04305, Q04177, P42945, P25635, P40362, Q06078, P33750, P40055, P32899, P47083, Q08492, P15646, P39990, Q06506, Q05498
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · resolution 4.3 · 29 distinct chains · 24% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | 5'ETS rRNA | rna | 408 | — | — |
| 1 | 18S rRNA 5' domain start | rna | 15 | — | — |
| 2 | U3 snoRNA | rna | 146 | — | — |
| H | Utp17 | protein | 834 | 8% helix, 34% strand | — |
| I | Utp8 | protein | 487 | 25% helix, 23% strand | — |
| J | Utp15 | protein | 493 | 23% helix, 28% strand | Q04305 |
| K | Utp9 | protein | 123 | 75% helix, 0% strand | — |
| L | Utp5 | protein | 473 | 18% helix, 36% strand | Q04177 |
| M | Utp10 | protein | 431 | 65% helix, 0% strand | P42945 |
| N | Utp4 | protein | 678 | 5% helix, 40% strand | — |
| O | Utp1 | protein | 832 | 15% helix, 34% strand | P25635 |
| P | Utp6 | protein | 359 | 77% helix, 0% strand | — |
| Q | Utp12 | protein | 862 | 22% helix, 32% strand | — |
| R | Utp13 | protein | 725 | 18% helix, 29% strand | — |
| S | Utp18 | protein | 481 | 12% helix, 32% strand | P40362 |
| T | Utp21 | protein | 812 | 13% helix, 41% strand | Q06078 |
| U | Sof1 | protein | 407 | 14% helix, 34% strand | P33750 |
| W | Utp7 | protein | 385 | 8% helix, 36% strand | P40055 |
| Z | Imp3 | protein | 169 | 46% helix, 6% strand | P32899 |
| A | Mpp10 | protein | 31 | 77% helix, 0% strand | P47083 |
| D | Bud21 | protein | 25 | 44% helix, 0% strand | Q08492 |
| a | Nop56 | protein | 368 | 59% helix, 7% strand | — |
| b | Nop58 | protein | 425 | 54% helix, 3% strand | — |
| c | Nop1.1 (EC 2.1.1.-) | protein | 203 | 28% helix, 25% strand | P15646 |
| d | Nop1.1 (EC 2.1.1.-) | protein | 228 | 23% helix, 26% strand | P15646 |
| e, f | Snu13 | protein | 121 | 45% helix, 15% strand | P39990 |
| g | Rrp9 | protein | 391 | 3% helix, 42% strand | Q06506 |
| l | Utp24 | protein | 25 | 12% helix, 0% strand | Q05498 |
| x | Unidentified fragment | protein | 24 | 92% helix, 0% strand | — |
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 | 1104 | 0.85 | 0.86 | 149 | empty |
| 2 | 1173 | 0.84 | 0.85 | 167 | empty |
| 3 | 1041 | 0.83 | 0.84 | 151 | empty |
| 4 | 539 | 0.83 | 0.89 | 101 | empty |
| 5 | 740 | 0.83 | 0.87 | 120 | empty |
Interfaces
98 interfaces between chains.
- 0–2 · 1424 Ų buried · 180 hydrogen bonds · nucleic-nucleic
- 0–S · 1339 Ų buried · 17 hydrogen bonds · protein-nucleic
- J–L · 1259 Ų buried · 9 hydrogen bonds · protein-protein
- O–T · 1220 Ų buried · 2 hydrogen bonds · protein-protein
- 0–O · 1128 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 6ND4 · Conformational switches control early maturation of the eukaryotic small ribosomal subunit · the same entry in another collection · chain M against M, 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 Q04305
- Every structure of UniProt Q04177
- Every structure of UniProt P42945
- Every structure of UniProt P25635
- Every structure of UniProt P40362
- Every structure of UniProt Q06078
- Every structure of UniProt P33750
- Every structure of UniProt P40055
- Every structure of UniProt P32899
- Every structure of UniProt P47083
- Every structure of UniProt Q08492
- Every structure of UniProt P15646
- Every structure of UniProt P39990
- Every structure of UniProt Q06506
- Every structure of UniProt Q05498
- Elsewhere: RCSB PDB 6ND4 · PDBe 6ND4 · UniProt Q04305 · UniProt Q04177 · UniProt P42945 · UniProt P25635 · UniProt P40362 · UniProt Q06078 · UniProt P33750 · UniProt P40055 · UniProt P32899 · UniProt P47083 · UniProt Q08492 · UniProt P15646 · UniProt P39990 · UniProt Q06506 · UniProt Q05498
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