Research workbench
Yeast nucleolar pre-60S ribosomal subunit (state 2)
Analyse Yeast nucleolar pre-60S ribosomal subunit (state 2) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C0F
- Type
- protein + RNA
- Length
- 8,925 residues
- Chains
- 43
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA miscrna; 5.8S rRNA; ITS2; Ribosome…
- EC
- 3.6.4.13
- UniProt
- P53136, P14126, P10664, P10962, Q02326, P05737, P17076, P38805, P38779, Q12690, P36105, P05748, P26784, P05740, P0CX49, P0CX23, P0CX41, Q02892, P05743, P40007, P36080, P38061, P05744, P0CX84, P05745, P49166, P53261, P53927, Q03532, P40693, Q07915, P38789, Q06511, Q12522, P35178
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 43 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA miscrna | rna | 1357 | — | — |
| 2 | 5.8S rRNA | rna | 158 | — | — |
| 6 | ITS2 | rna | 87 | — | — |
| A | Ribosome biogenesis protein NSA1 | protein | 394 | 3% helix, 43% strand | P53136 |
| B | 60S ribosomal protein L3 | protein | 324 | 15% helix, 32% strand | P14126 |
| C | 60S ribosomal protein L4-a | protein | 314 | 36% helix, 10% strand | P10664 |
| D | Protein MAK16 | protein | 190 | 47% helix, 14% strand | P10962 |
| E | 60S ribosomal protein L6-a | protein | 170 | 27% helix, 18% strand | Q02326 |
| F | 60S ribosomal protein L7-a | protein | 242 | 52% helix, 11% strand | P05737 |
| G | 60S ribosomal protein L8-a | protein | 187 | 45% helix, 9% strand | P17076 |
| I | Ribosome production factor 1 | protein | 288 | 31% helix, 27% strand | P38805 |
| K | Proteasome-interacting protein CIC1 | protein | 260 | 43% helix, 21% strand | P38779 |
| L | 60S ribosomal protein L13-a | protein | 106 | 43% helix, 12% strand | Q12690 |
| M | 60S ribosomal protein L14-a | protein | 128 | 42% helix, 24% strand | P36105 |
| N | 60S ribosomal protein L15-a | protein | 176 | 41% helix, 19% strand | P05748 |
| O | 60S ribosomal protein L16-a | protein | 184 | 60% helix, 14% strand | P26784 |
| P | 60S ribosomal protein L17-a | protein | 124 | 35% helix, 27% strand | P05740 |
| Q | 60S ribosomal protein L18-a | protein | 132 | 38% helix, 19% strand | P0CX49 |
| S | 60S ribosomal protein L20-a | protein | 171 | 22% helix, 30% strand | P0CX23 |
| V | 60S ribosomal protein L23-a | protein | 122 | 9% helix, 42% strand | P0CX41 |
| W | Nucleolar GTP-binding protein 1 | protein | 98 | 32% helix, 4% strand | Q02892 |
| Y | 60S ribosomal protein L26-a | protein | 126 | 30% helix, 32% strand | P05743 |
| 7 | Nucleolar protein 16 | protein | 156 | 40% helix, 1% strand | P40007 |
| 8 | Ribosomal RNA-processing protein 14 | protein | 98 | 89% helix, 0% strand | P36080 |
| b | Ribosome biogenesis protein BRX1 | protein | 242 | 30% helix, 26% strand | — |
| e | 60S ribosomal protein L32 | protein | 114 | 21% helix, 12% strand | P38061 |
| f | 60S ribosomal protein L33-a | protein | 106 | 6% helix, 49% strand | P05744 |
| h | 60S ribosomal protein L35-a | protein | 119 | 60% helix, 3% strand | P0CX84 |
| i | 60S ribosomal protein L36-a | protein | 84 | 73% helix, 0% strand | P05745 |
| j | 60S ribosomal protein L37-a | protein | 72 | 21% helix, 8% strand | P49166 |
| x | BRX1-associated peptide | protein | 28 | 46% helix, 0% strand | — |
| m | RRNA-processing protein EBP2 | protein | 74 | 55% helix, 3% strand | — |
| n | Pescadillo homolog | protein | 341 | 47% helix, 7% strand | P53261 |
| o | Ribosome biogenesis protein 15 | protein | 133 | 29% helix, 26% strand | P53927 |
| p | ATP-dependent RNA helicase HAS1 (EC 3.6.4.13) | protein | 437 | 48% helix, 14% strand | Q03532 |
| q | Protein MAK11 | protein | 285 | 0% helix, 52% strand | — |
| s | Ribosome biogenesis protein ERB1 | protein | 157 | 41% helix, 1% strand | — |
| t | Ribosome biogenesis protein RLP7 | protein | 248 | 42% helix, 15% strand | P40693 |
| u | Ribosome biogenesis protein RLP24 | protein | 129 | 43% helix, 9% strand | Q07915 |
| v | Ribosome biogenesis protein SSF1 | protein | 225 | 23% helix, 27% strand | P38789 |
| w | Ribosomal RNA-processing protein 15 | protein | 70 | 84% helix, 0% strand | Q06511 |
| y | Eukaryotic translation initiation factor 6 | protein | 226 | 24% helix, 23% strand | Q12522 |
| z | Ribosomal RNA-processing protein 1 | protein | 243 | 77% helix, 0% strand | P35178 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains D, j, u
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 | 847 | 0.89 | 0.92 | 97 | empty |
| 2 | 1151 | 0.88 | 0.91 | 124 | empty |
| 3 | 750 | 0.88 | 0.92 | 74 | empty |
| 4 | 640 | 0.87 | 0.92 | 83 | empty |
| 5 | 978 | 0.87 | 0.88 | 92 | empty |
Interfaces
151 interfaces between chains.
- 1–C · 6989 Ų buried · 181 hydrogen bonds · protein-nucleic
- 1–B · 5292 Ų buried · 149 hydrogen bonds · protein-nucleic
- 1–N · 4546 Ų buried · 84 hydrogen bonds · protein-nucleic
- 1–2 · 4267 Ų buried · 333 hydrogen bonds · nucleic-nucleic
- 1–O · 3440 Ų buried · 75 hydrogen bonds · protein-nucleic
Compared structures
- 6C0F · Yeast nucleolar pre-60S ribosomal subunit (state 2) · the same entry in another collection · chain I against I, 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 P53136
- Every structure of UniProt P14126
- Every structure of UniProt P10664
- Every structure of UniProt P10962
- Every structure of UniProt Q02326
- Every structure of UniProt P05737
- Every structure of UniProt P17076
- Every structure of UniProt P38805
- Every structure of UniProt P38779
- Every structure of UniProt Q12690
- Every structure of UniProt P36105
- Every structure of UniProt P05748
- Every structure of UniProt P26784
- Every structure of UniProt P05740
- Every structure of UniProt P0CX49
- Every structure of UniProt P0CX23
- Every structure of UniProt P0CX41
- Every structure of UniProt Q02892
- Every structure of UniProt P05743
- Every structure of UniProt P40007
- Every structure of UniProt P36080
- Every structure of UniProt P38061
- Every structure of UniProt P05744
- Every structure of UniProt P0CX84
- Every structure of UniProt P05745
- Every structure of UniProt P49166
- Every structure of UniProt P53261
- Every structure of UniProt P53927
- Every structure of UniProt Q03532
- Every structure of UniProt P40693
- Every structure of UniProt Q07915
- Every structure of UniProt P38789
- Every structure of UniProt Q06511
- Every structure of UniProt Q12522
- Every structure of UniProt P35178
- Elsewhere: RCSB PDB 6C0F · PDBe 6C0F · UniProt P53136 · UniProt P14126 · UniProt P10664 · UniProt P10962 · UniProt Q02326 · UniProt P05737 · UniProt P17076 · UniProt P38805 · UniProt P38779 · UniProt Q12690 · UniProt P36105 · UniProt P05748 · UniProt P26784 · UniProt P05740 · UniProt P0CX49 · UniProt P0CX23 · UniProt P0CX41 · UniProt Q02892 · UniProt P05743 · UniProt P40007 · UniProt P36080 · UniProt P38061 · UniProt P05744 · UniProt P0CX84 · UniProt P05745 · UniProt P49166 · UniProt P53261 · UniProt P53927 · UniProt Q03532 · UniProt P40693 · UniProt Q07915 · UniProt P38789 · UniProt Q06511 · UniProt Q12522 · UniProt P35178
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