Research workbench
Structural snapshot of cytoplasmic pre-60S ribosomal particles bound with Nmd3, Lsg1, Tif6 and Reh1
Analyse Structural snapshot of cytoplasmic pre-60S ribosomal particles bound with Nmd3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H4P
- Type
- protein + RNA
- Length
- 9,802 residues
- Chains
- 44
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.07
- Source
- Saccharomyces cerevisiae; Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Molecule
- 25S ribosomal RNA; 5S ribosomal RNA; 5.8S ribosomal RNA; 60S ribosomal protein L2-A; 60S…
- UniProt
- P0CX45, P14126, P10664, P26321, Q02326, P05737, P17076, P05738, P0C0W9, Q12690, P36105, P05748, P26784, P05740, P0CX49, P0CX82, P0CX23, Q02753, P05749, P0CX41, P04449, P04456, P05743, P0C2H6, P02406, P05747, P14120, P0C2H8, P38061, P05744, P87262, P0CX84, P05745, P49166, P49167, P04650, P0CX27, P0CX25, P38861, Q12522, Q06709
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · resolution 3.07 · 44 distinct chains · 29% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | 25S ribosomal RNA | rna | 3091 | — | — |
| 3 | 5S ribosomal RNA | rna | 121 | — | — |
| 4 | 5.8S ribosomal RNA | rna | 158 | — | — |
| A | 60S ribosomal protein L2-A | protein | 246 | 7% helix, 26% strand | P0CX45 |
| B | 60S ribosomal protein L3 | protein | 386 | 12% helix, 27% strand | P14126 |
| C | 60S ribosomal protein L4-A | protein | 361 | 26% helix, 11% strand | P10664 |
| D | 60S ribosomal protein L5 | protein | 296 | 43% helix, 9% strand | P26321 |
| E | 60S ribosomal protein L6-A | protein | 156 | 18% helix, 19% strand | Q02326 |
| F | 60S ribosomal protein L7-A | protein | 222 | 50% helix, 14% strand | P05737 |
| G | 60S ribosomal protein L8-A | protein | 233 | 45% helix, 7% strand | P17076 |
| H | 60S ribosomal protein L9-A | protein | 191 | 19% helix, 40% strand | P05738 |
| J | 60S ribosomal protein L11-A | protein | 169 | 24% helix, 19% strand | P0C0W9 |
| L | 60S ribosomal protein L13-A | protein | 193 | 36% helix, 8% strand | Q12690 |
| M | 60S ribosomal protein L14-A | protein | 136 | 40% helix, 22% strand | P36105 |
| N | 60S ribosomal protein L15-A | protein | 203 | 36% helix, 17% strand | P05748 |
| O | 60S ribosomal protein L16-A | protein | 197 | 53% helix, 11% strand | P26784 |
| P | 60S ribosomal protein L17-A | protein | 183 | 28% helix, 27% strand | P05740 |
| Q | 60S ribosomal protein L18-A | protein | 185 | 29% helix, 14% strand | P0CX49 |
| R | 60S ribosomal protein L19-A | protein | 156 | 62% helix, 3% strand | P0CX82 |
| S | 60S ribosomal protein L20-A | protein | 172 | 22% helix, 28% strand | P0CX23 |
| T | 60S ribosomal protein L21-A | protein | 159 | 13% helix, 23% strand | Q02753 |
| U | 60S ribosomal protein L22-A | protein | 100 | 29% helix, 32% strand | P05749 |
| V | 60S ribosomal protein L23-A | protein | 136 | 10% helix, 32% strand | P0CX41 |
| W | 60S ribosomal protein L24-A | protein | 64 | 25% helix, 19% strand | P04449 |
| X | 60S ribosomal protein L25 | protein | 121 | 23% helix, 23% strand | P04456 |
| Y | 60S ribosomal protein L26-A | protein | 126 | 27% helix, 32% strand | P05743 |
| Z | 60S ribosomal protein L27-A | protein | 135 | 19% helix, 27% strand | P0C2H6 |
| a | 60S ribosomal protein L28 | protein | 148 | 17% helix, 14% strand | P02406 |
| b | 60S ribosomal protein L29 | protein | 58 | 50% helix, 2% strand | P05747 |
| c | 60S ribosomal protein L30 | protein | 97 | 41% helix, 16% strand | P14120 |
| d | 60S ribosomal protein L31-A | protein | 109 | 22% helix, 26% strand | P0C2H8 |
| e | 60S ribosomal protein L32 | protein | 127 | 19% helix, 8% strand | P38061 |
| f | 60S ribosomal protein L33-A | protein | 106 | 4% helix, 48% strand | P05744 |
| g | 60S ribosomal protein L34-A | protein | 112 | 29% helix, 11% strand | P87262 |
| h | 60S ribosomal protein L35-A | protein | 119 | 54% helix, 3% strand | P0CX84 |
| i | 60S ribosomal protein L36-A | protein | 99 | 52% helix, 0% strand | P05745 |
| j | 60S ribosomal protein L37-A | protein | 87 | 23% helix, 7% strand | P49166 |
| k | 60S ribosomal protein L38 | protein | 77 | 21% helix, 43% strand | P49167 |
| l | 60S ribosomal protein L39 | protein | 50 | 28% helix, 0% strand | P04650 |
| o | 60S ribosomal protein L42-A | protein | 95 | 9% helix, 31% strand | P0CX27 |
| p | 60S ribosomal protein L43-A | protein | 91 | 41% helix, 13% strand | P0CX25 |
| w | 60S ribosomal export protein NMD3 | protein | 248 | 20% helix, 37% strand | P38861 |
| y | Eukaryotic translation initiation factor 6 | protein | 227 | 29% helix, 23% strand | Q12522 |
| z | Cytoplasmic 60S subunit biogenesis factor REH1 | protein | 56 | 57% helix, 0% strand | Q06709 |
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 | 888 | 0.90 | 0.93 | 111 | empty |
| 2 | 729 | 0.88 | 0.93 | 85 | empty |
| 3 | 902 | 0.88 | 0.91 | 119 | empty |
| 4 | 999 | 0.88 | 0.90 | 101 | empty |
| 5 | 999 | 0.88 | 0.90 | 78 | empty |
Interfaces
134 interfaces between chains.
- 1–B · 9041 Ų buried · 183 hydrogen bonds · protein-nucleic
- 1–C · 8081 Ų buried · 152 hydrogen bonds · protein-nucleic
- 1–N · 7443 Ų buried · 150 hydrogen bonds · protein-nucleic
- 1–A · 7257 Ų buried · 170 hydrogen bonds · protein-nucleic
- 1–4 · 5179 Ų buried · 272 hydrogen bonds · nucleic-nucleic
Compared structures
- P0CX45 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L2-a (P0CX45) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P14126 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L3 (P14126) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P05748 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L15-a (P05748) · a predicted model of the same protein · chain N against A, TM-score 0.99
- P05737 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L7-a (P05737) · a predicted model of the same protein · chain F against A, TM-score 0.98
- Q12522 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 6 (Q12522) · a predicted model of the same protein · chain y against A, TM-score 0.98
- P26784 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L16-a (P26784) · a predicted model of the same protein · chain O against A, TM-score 0.98
- P05749 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L22-a (P05749) · a predicted model of the same protein · chain U against A, TM-score 0.98
- P0CX25 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L43-a (P0CX25) · a predicted model of the same protein · chain p against A, TM-score 0.98
- P0C2H6 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L27-a (P0C2H6) · a predicted model of the same protein · chain Z against A, TM-score 0.98
- P05743 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L26-a (P05743) · a predicted model of the same protein · chain Y against A, TM-score 0.98
- P38061 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L32 (P38061) · a predicted model of the same protein · chain e against A, TM-score 0.98
- P0C0W9 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L11-a (P0C0W9) · a predicted model of the same protein · chain J against A, TM-score 0.97
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 P0CX45
- Every structure of UniProt P14126
- Every structure of UniProt P10664
- Every structure of UniProt P26321
- Every structure of UniProt Q02326
- Every structure of UniProt P05737
- Every structure of UniProt P17076
- Every structure of UniProt P05738
- Every structure of UniProt P0C0W9
- 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 P0CX82
- Every structure of UniProt P0CX23
- Every structure of UniProt Q02753
- Every structure of UniProt P05749
- Every structure of UniProt P0CX41
- Every structure of UniProt P04449
- Every structure of UniProt P04456
- Every structure of UniProt P05743
- Every structure of UniProt P0C2H6
- Every structure of UniProt P02406
- Every structure of UniProt P05747
- Every structure of UniProt P14120
- Every structure of UniProt P0C2H8
- Every structure of UniProt P38061
- Every structure of UniProt P05744
- Every structure of UniProt P87262
- Every structure of UniProt P0CX84
- Every structure of UniProt P05745
- Every structure of UniProt P49166
- Every structure of UniProt P49167
- Every structure of UniProt P04650
- Every structure of UniProt P0CX27
- Every structure of UniProt P0CX25
- Every structure of UniProt P38861
- Every structure of UniProt Q12522
- Every structure of UniProt Q06709
- Elsewhere: RCSB PDB 5H4P · PDBe 5H4P · UniProt P0CX45 · UniProt P14126 · UniProt P10664 · UniProt P26321 · UniProt Q02326 · UniProt P05737 · UniProt P17076 · UniProt P05738 · UniProt P0C0W9 · UniProt Q12690 · UniProt P36105 · UniProt P05748 · UniProt P26784 · UniProt P05740 · UniProt P0CX49 · UniProt P0CX82 · UniProt P0CX23 · UniProt Q02753 · UniProt P05749 · UniProt P0CX41 · UniProt P04449 · UniProt P04456 · UniProt P05743 · UniProt P0C2H6 · UniProt P02406 · UniProt P05747 · UniProt P14120 · UniProt P0C2H8 · UniProt P38061 · UniProt P05744 · UniProt P87262 · UniProt P0CX84 · UniProt P05745 · UniProt P49166 · UniProt P49167 · UniProt P04650 · UniProt P0CX27 · UniProt P0CX25 · UniProt P38861 · UniProt Q12522 · UniProt Q06709
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