Research workbench
AlphaFold monomer V2.0 prediction for 60S ribosomal export protein NMD3 (P38861)
Analyse AlphaFold monomer V2.0 prediction for 60S ribosomal export protein NMD3 (P38861) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- Accession
- P38861
- Type
- protein
- Length
- 518 residues
- Chains
- 1
- Collection
- MolNFT v1 / AlphaFold
- Contract
- 0xBf7491af3407816DFa88a5EA4c82e8A2B1D721eD
- Owner
- 0x6Ed09D80e98fE15DE51C9E7a8896AbF1f2365C3e
- Molecule
- 60S ribosomal export protein NMD3
- UniProt
- P38861
- Pockets
- 6 · best druggability 0.73
Structure
1 distinct chain · 23% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 60S ribosomal export protein NMD3 | protein | 518 | 23% helix, 33% strand | P38861 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.73 | 0.83 | 40 | empty |
| 2 | 587 | 0.68 | 0.78 | 49 | empty |
| 3 | 236 | 0.55 | 0.78 | 23 | empty |
| 4 | 116 | 0.47 | 0.79 | 21 | empty |
| 5 | 113 | 0.44 | 0.78 | 22 | empty |
Compared structures
- 6N8M · Cryo-EM structure of pre-Lsg1 (PL) pre-60S ribosomal subunit · an experimental structure of the same protein · chain A against V, TM-score 0.72
- 6N8L · Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunit · an experimental structure of the same protein · chain A against v, TM-score 0.66
- 5T62 · Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome… · an experimental structure of the same protein · chain A against V, TM-score 0.65
- 6RZZ · Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles · an experimental structure of the same protein · chain A against w, TM-score 0.62
- 6QIK · Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles · an experimental structure of the same protein · chain A against w, TM-score 0.62
- 6S05 · Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles · an experimental structure of the same protein · chain A against w, TM-score 0.62
- 6QTZ · Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles · an experimental structure of the same protein · chain A against w, TM-score 0.62
- 6N8N · Cryo-EM structure of Lsg1-engaged (LE) pre-60S ribosomal subunit · an experimental structure of the same protein · chain A against V, TM-score 0.61
- 6N8O · Cryo-EM structure of Rpl10-inserted (RI) pre-60S ribosomal subunit · an experimental structure of the same protein · chain A against V, TM-score 0.61
- 6N8K · Cryo-EM structure of early cytoplasmic-immediate (ECI) pre-60S ribosomal subunit · an experimental structure of the same protein · chain A against v, TM-score 0.48
- 5T6R · Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome… · an experimental structure of the same protein · chain A against V, TM-score 0.48
- 5H4P · Structural snapshot of cytoplasmic pre-60S ribosomal particles bound with Nmd3, Lsg1… · an experimental structure of the same protein · chain A against w, TM-score 0.47
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 P38861
- Elsewhere: UniProt P38861 · AlphaFold DB P38861
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