Research workbench
Structure of the yeast kluyveromyces lactis small ribosomal subunit in complex with the cricket paralysis virus ires.
Analyse Structure of the yeast kluyveromyces lactis small ribosomal subunit in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IT9
- Type
- protein + RNA
- Length
- 6,820 residues
- Chains
- 35
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal protein US2; Ribosomal protein ES1; Ribosomal protein US5; Ribosomal protein…
- UniProt
- Q6CN12, Q6CWD0, Q6CKL3, Q6CRK7, Q6CWJ2, Q6CRA3, Q6CM04, Q6CTD6, Q6CMG3, Q6CM18, Q6CVZ5, Q6CX80, Q6CLU4, Q6CJK0, P27069, Q6CKV4, Q875N2, Q6CWU3, Q6CWT9, Q6CXM0, Q6CIM1, Q6CXT6, Q6CW21, Q875M3, Q6CU44, Q6CW78, Q6CS01, Q6CNL2, P33285, Q6CPG3, Q6CUH5, P69061, Q6CNI7
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 35 distinct chains · 29% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal protein US2 | protein | 206 | 32% helix, 9% strand | Q6CN12 |
| B | Ribosomal protein ES1 | protein | 214 | 29% helix, 25% strand | Q6CWD0 |
| C | Ribosomal protein US5 | protein | 217 | 31% helix, 25% strand | Q6CKL3 |
| D | Ribosomal protein US3 | protein | 223 | 32% helix, 27% strand | Q6CRK7 |
| E | Ribosomal protein ES4 | protein | 260 | 17% helix, 27% strand | Q6CWJ2 |
| F | Ribosomal protein US7 | protein | 206 | 48% helix, 6% strand | Q6CRA3 |
| G | Ribosomal protein ES6 | protein | 226 | 26% helix, 27% strand | Q6CM04 |
| H | Ribosomal protein ES7 | protein | 184 | 35% helix, 22% strand | Q6CTD6 |
| I | Ribosomal protein ES8 | protein | 188 | 26% helix, 18% strand | Q6CMG3 |
| J | Ribosomal protein US4 | protein | 182 | 46% helix, 2% strand | Q6CM18 |
| K | Ribosomal protein ES10 | protein | 96 | 43% helix, 15% strand | Q6CVZ5 |
| L | Ribosomal protein US17 | protein | 155 | 3% helix, 26% strand | Q6CX80 |
| M | Ribosomal protein ES12 | protein | 122 | 43% helix, 7% strand | Q6CLU4 |
| N | Ribosomal protein US15 | protein | 150 | 57% helix, 0% strand | Q6CJK0 |
| O | Ribosomal protein US14 | protein | 127 | 27% helix, 20% strand | P27069 |
| P | Ribosomal protein US19 | protein | 123 | 29% helix, 13% strand | Q6CKV4 |
| Q | Ribosomal protein US9 | protein | 141 | 36% helix, 21% strand | Q875N2 |
| R | Ribosomal protein ES17 | protein | 129 | 49% helix, 2% strand | Q6CWU3 |
| S | Ribosomal protein US13 | protein | 145 | 38% helix, 5% strand | Q6CWT9 |
| T | Ribosomal protein ES19 | protein | 143 | 48% helix, 8% strand | Q6CXM0 |
| U | Ribosomal protein US10 | protein | 106 | 25% helix, 42% strand | Q6CIM1 |
| V | Ribosomal protein ES21 | protein | 87 | 21% helix, 18% strand | Q6CXT6 |
| W | Ribosomal protein US8 | protein | 129 | 34% helix, 22% strand | Q6CW21 |
| X | Ribosomal protein US21 | protein | 145 | 23% helix, 26% strand | Q875M3 |
| Y | Ribosomal protein ES24 | protein | 134 | 41% helix, 26% strand | Q6CU44 |
| Z | Ribosomal protein ES25 | protein | 70 | 33% helix, 10% strand | Q6CW78 |
| a | Ribosomal protein ES26 | protein | 100 | 17% helix, 20% strand | Q6CS01 |
| b | Ribosomal protein ES27 | protein | 82 | 7% helix, 22% strand | Q6CNL2 |
| c | Ribosomal protein ES28 | protein | 63 | 0% helix, 46% strand | P33285 |
| d | Ribosomal protein ES29 | protein | 53 | 19% helix, 11% strand | Q6CPG3 |
| e | Ribosomal protein ES30 | protein | 55 | 33% helix, 0% strand | Q6CUH5 |
| f | Ribosomal protein ES31 | protein | 69 | 0% helix, 14% strand | P69061 |
| g | Ribosomal protein RACK1 | protein | 318 | 0% helix, 51% strand | Q6CNI7 |
| 2 | 18S ribosomal RNA | rna | 1780 | — | — |
| i | Cricket paralysis virus ires RNA | rna | 192 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 80 copies · chains G, 2, N, T, X, i, a, E, D, I, Q, S
- ZN · Zinc ion · metal · 3 copies · chains a, b, f
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 | 1158 | 0.89 | 0.91 | 93 | MG |
| 2 | 942 | 0.88 | 0.91 | 91 | MG |
| 3 | 815 | 0.88 | 0.92 | 88 | empty |
| 4 | 716 | 0.88 | 0.93 | 79 | MG |
| 5 | 998 | 0.88 | 0.90 | 84 | MG |
Interfaces
103 interfaces between chains.
- G–2 · 5677 Ų buried · 130 hydrogen bonds · protein-nucleic
- E–2 · 4458 Ų buried · 84 hydrogen bonds · protein-nucleic
- I–2 · 4312 Ų buried · 121 hydrogen bonds · protein-nucleic
- X–2 · 4002 Ų buried · 90 hydrogen bonds · protein-nucleic
- J–2 · 3648 Ų buried · 61 hydrogen bonds · protein-nucleic
Compared structures
- 5IT9 · Structure of the yeast Kluyveromyces lactis small ribosomal subunit in complex with the… · the same entry in another collection · chain J against J, 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 Q6CN12
- Every structure of UniProt Q6CWD0
- Every structure of UniProt Q6CKL3
- Every structure of UniProt Q6CRK7
- Every structure of UniProt Q6CWJ2
- Every structure of UniProt Q6CRA3
- Every structure of UniProt Q6CM04
- Every structure of UniProt Q6CTD6
- Every structure of UniProt Q6CMG3
- Every structure of UniProt Q6CM18
- Every structure of UniProt Q6CVZ5
- Every structure of UniProt Q6CX80
- Every structure of UniProt Q6CLU4
- Every structure of UniProt Q6CJK0
- Every structure of UniProt P27069
- Every structure of UniProt Q6CKV4
- Every structure of UniProt Q875N2
- Every structure of UniProt Q6CWU3
- Every structure of UniProt Q6CWT9
- Every structure of UniProt Q6CXM0
- Every structure of UniProt Q6CIM1
- Every structure of UniProt Q6CXT6
- Every structure of UniProt Q6CW21
- Every structure of UniProt Q875M3
- Every structure of UniProt Q6CU44
- Every structure of UniProt Q6CW78
- Every structure of UniProt Q6CS01
- Every structure of UniProt Q6CNL2
- Every structure of UniProt P33285
- Every structure of UniProt Q6CPG3
- Every structure of UniProt Q6CUH5
- Every structure of UniProt P69061
- Every structure of UniProt Q6CNI7
- Elsewhere: RCSB PDB 5IT9 · PDBe 5IT9 · UniProt Q6CN12 · UniProt Q6CWD0 · UniProt Q6CKL3 · UniProt Q6CRK7 · UniProt Q6CWJ2 · UniProt Q6CRA3 · UniProt Q6CM04 · UniProt Q6CTD6 · UniProt Q6CMG3 · UniProt Q6CM18 · UniProt Q6CVZ5 · UniProt Q6CX80 · UniProt Q6CLU4 · UniProt Q6CJK0 · UniProt P27069 · UniProt Q6CKV4 · UniProt Q875N2 · UniProt Q6CWU3 · UniProt Q6CWT9 · UniProt Q6CXM0 · UniProt Q6CIM1 · UniProt Q6CXT6 · UniProt Q6CW21 · UniProt Q875M3 · UniProt Q6CU44 · UniProt Q6CW78 · UniProt Q6CS01 · UniProt Q6CNL2 · UniProt P33285 · UniProt Q6CPG3 · UniProt Q6CUH5 · UniProt P69061 · UniProt Q6CNI7
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