MolNFT v1 · #126279 · protein
High-resolution structure of human collapsin response mediator protein 2
5LXX · Dihydropyrimidinase-related protein 2: “High-resolution structure of human collapsin response mediator protein 2”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.85). MolNFT v1 #126279 on GenesisL1: 3D structure…
- PDB
- 5LXX
- Type
- protein
- Length
- 953 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropyrimidinase-related protein 2
- UniProt
- Q16555
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropyrimidinase-related protein 2 | protein | 477 | 37% helix, 23% strand | Q16555 |
| B | Dihydropyrimidinase-related protein 2 | protein | 476 | 36% helix, 24% strand | Q16555 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 811 | 0.85 | 0.88 | 89 | empty |
| 2 | 267 | 0.67 | 0.83 | 36 | BTB |
| 3 | 275 | 0.67 | 0.83 | 42 | BTB |
| 4 | 165 | 0.59 | 0.83 | 22 | empty |
| 5 | 157 | 0.56 | 0.82 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1243 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5LXX · High-resolution structure of human collapsin response mediator protein 2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q16555 · AlphaFold monomer V2.0 prediction for dihydropyrimidinase-related protein 2 (Q16555) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q16555
- Elsewhere: RCSB PDB 5LXX · PDBe 5LXX · UniProt Q16555
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