MolNFT v1 · #54539 · protein + RNA
Crystal structure of the rrm domain of mouse deleted in azoospermia-like in complex with mvh RNA, uguuc
2XS5: “Crystal structure of the rrm domain of mouse deleted in azoospermia-like in complex with mvh RNA, uguuc”. X-ray diffraction, 1 pocket (best druggability 0.69). MolNFT v1 #54539 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2XS5
- Type
- protein + RNA
- Length
- 174 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deleted in azoospermia-like; 5'-R(*UP*GP*UP*UP*CP)-3'
- UniProt
- Q64368
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deleted in azoospermia-like | protein | 82 | 15% helix, 46% strand | Q64368 |
| B | Deleted in azoospermia-like | protein | 83 | 18% helix, 46% strand | Q64368 |
| C | 5'-R(*UP*GP*UP*UP*CP)-3' | rna | 5 | — | — |
| D | 5'-R(*UP*GP*UP*UP*CP)-3' | rna | 4 | — | — |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 519 | 0.69 | 0.80 | 45 | empty |
Interfaces
5 interfaces between chains.
- A–C · 723 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–D · 624 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–B · 352 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 117 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–D · 116 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 2XS5 · Crystal structure of the RRM domain of mouse Deleted in azoospermia- like in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q64368 · AlphaFold monomer V2.0 prediction for deleted in azoospermia-like (Q64368) · a predicted model of the same protein · chain A 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 Q64368
- Elsewhere: RCSB PDB 2XS5 · PDBe 2XS5 · UniProt Q64368
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