Research workbench
Structure of the large subunit of the mammalian mitoribosome, part 2 of 2
Analyse Structure of the large subunit of the mammalian mitoribosome, part 2 of 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4V1A
- Type
- protein
- Length
- 3,936 residues
- Chains
- 23
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitoribosomal protein ML37, MRPL37; Mitoribosomal protein ML38, MRPL38; Mitoribosomal…
- UniProt
- F1RW03, F1RK59, F1S8U4, F1SR64, F1SRT0, I3L9H6, F1S9B7, F1SLH8, W5IDC0, F1SD95, F1RRH6
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.73
Structure
electron microscopy · 23 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a | Mitoribosomal protein ML37, MRPL37 | protein | 393 | 27% helix, 26% strand | — |
| b | Mitoribosomal protein ML38, MRPL38 | protein | 354 | 25% helix, 18% strand | F1RW03 |
| c | Mitoribosomal protein ML39, MRPL39 | protein | 295 | 34% helix, 27% strand | — |
| d | Mitoribosomal protein ML40, MRPL40 | protein | 99 | 62% helix, 4% strand | F1RK59 |
| e | Mitoribosomal protein ML41, MRPL41 | protein | 121 | 19% helix, 5% strand | — |
| f | Mitoribosomal protein ML42, MRPL42 | protein | 108 | 23% helix, 11% strand | — |
| g | Mitoribosomal protein ML43, MRPL43 | protein | 148 | 26% helix, 18% strand | F1S8U4 |
| h | Mitoribosomal protein ML44, MRPL44 | protein | 289 | 58% helix, 9% strand | F1SR64 |
| i | Mitoribosomal protein ML45, MRPL45 | protein | 242 | 26% helix, 24% strand | — |
| j | Mitoribosomal protein ML46, MRPL46 | protein | 217 | 33% helix, 29% strand | F1SRT0 |
| k | Mitoribosomal protein ML48, MRPL48 | protein | 131 | 23% helix, 36% strand | — |
| l | Mitoribosomal protein ML49, MRPL49 | protein | 133 | 25% helix, 20% strand | — |
| m | Mitoribosomal protein ML50, MRPL50 | protein | 109 | 41% helix, 6% strand | I3L9H6 |
| n | Mitoribosomal protein ML51, MRPL51 | protein | 97 | 47% helix, 0% strand | — |
| o | Mitoribosomal protein ML52, MRPL52 | protein | 94 | 63% helix, 0% strand | F1S9B7 |
| p | Mitoribosomal protein ML53, MRPL53 | protein | 97 | 36% helix, 27% strand | F1SLH8 |
| q | Mitoribosomal protein ML54, MRPL54 | protein | 37 | 38% helix, 0% strand | — |
| t | Mitoribosomal protein ML63, MRPL57, MRP63 | protein | 94 | 50% helix, 1% strand | — |
| u | Mitoribosomal protein ML62, MRPL58, ICT1 | protein | 151 | 36% helix, 17% strand | W5IDC0 |
| v | Mitoribosomal protein ML64, MRPL59, CRIF1 | protein | 131 | 68% helix, 0% strand | F1SD95 |
| w | Mitoribosomal protein ML65, MRPS30 | protein | 387 | 34% helix, 22% strand | — |
| x | Mitoribosomal protein ML66, MRPS18A | protein | 162 | 23% helix, 11% strand | F1RRH6 |
| z | Unassigned secondary structure elements | protein | 47 | 70% helix, 6% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains x
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.73 | 0.77 | 78 | empty |
| 2 | 507 | 0.72 | 0.81 | 66 | empty |
| 3 | 534 | 0.70 | 0.79 | 49 | empty |
| 4 | 365 | 0.70 | 0.82 | 38 | empty |
| 5 | 164 | 0.67 | 0.87 | 25 | empty |
Interfaces
29 interfaces between chains.
- d–j · 2222 Ų buried · 28 hydrogen bonds · protein-protein
- g–h · 1568 Ų buried · 21 hydrogen bonds · protein-protein
- a–w · 1507 Ų buried · 14 hydrogen bonds · protein-protein
- d–k · 1412 Ų buried · 12 hydrogen bonds · protein-protein
- b–u · 1139 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4V1A · Structure of the large subunit of the mammalian mitoribosome, part 2 of 2 · the same entry in another collection · chain a against a, 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 F1RW03
- Every structure of UniProt F1RK59
- Every structure of UniProt F1S8U4
- Every structure of UniProt F1SR64
- Every structure of UniProt F1SRT0
- Every structure of UniProt I3L9H6
- Every structure of UniProt F1S9B7
- Every structure of UniProt F1SLH8
- Every structure of UniProt W5IDC0
- Every structure of UniProt F1SD95
- Every structure of UniProt F1RRH6
- Elsewhere: RCSB PDB 4V1A · PDBe 4V1A · UniProt F1RW03 · UniProt F1RK59 · UniProt F1S8U4 · UniProt F1SR64 · UniProt F1SRT0 · UniProt I3L9H6 · UniProt F1S9B7 · UniProt F1SLH8 · UniProt W5IDC0 · UniProt F1SD95 · UniProt F1RRH6
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