MolNFT v1 · #141481 · protein
Crystal structure of human LRRTM2 in complex with neurexin 1BETA
5Z8Y · Leucine-rich repeat transmembrane neuronal protein 2: “Crystal structure of human LRRTM2 in complex with neurexin 1BETA”. X-ray diffraction, 4 ligands (NAG, FUC, CA), 10 pockets (best druggability 0.85). MolNFT v1 #141481 on…
- PDB
- 5Z8Y
- Type
- protein
- Length
- 2,024 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine-rich repeat transmembrane neuronal protein 2; Neurexin-1-beta
- UniProt
- O43300, P58400
- Ligands
- NAG, FUC, CA, ZN
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Leucine-rich repeat transmembrane neuronal protein 2 | protein | 328 | 9% helix, 17% strand | O43300 |
| B, D, F, H | Neurexin-1-beta | protein | 178 | 3% helix, 52% strand | P58400 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains B, D, F, H, A, C, E, G
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains B, D, F, H
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D, E, F, G, H
- ZN · Zinc ion · metal · 2 copies · chains A, E, C, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1145 | 0.85 | 0.86 | 109 | empty |
| 2 | 1200 | 0.85 | 0.86 | 110 | empty |
| 3 | 674 | 0.70 | 0.78 | 63 | empty |
| 4 | 645 | 0.69 | 0.78 | 61 | empty |
| 5 | 311 | 0.58 | 0.77 | 34 | empty |
Interfaces
8 interfaces between chains.
- A–C · 1560 Ų buried · 6 hydrogen bonds · protein-protein
- E–G · 1541 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 473 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 471 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 470 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 16 glycan (disulfide, N-glycosylation).
Compared structures
- 5Z8Y · Crystal structure of human LRRTM2 in complex with Neurexin 1beta · the same entry in another collection · chain D against D, TM-score 1.00
- O43300 · AlphaFold monomer V2.0 prediction for leucine-rich repeat transmembrane neuronal protein… · a predicted model of the same protein · chain A against A, TM-score 0.99
- P58400 · AlphaFold monomer V2.0 prediction for neurexin-1-beta (P58400) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 O43300
- Every structure of UniProt P58400
- Elsewhere: RCSB PDB 5Z8Y · PDBe 5Z8Y · UniProt O43300 · UniProt P58400
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