MolNFT v1 · #17203 · protein
The ligand-binding face of the semaphorins revealed by the high resolution crystal structure of SEMA4D
1OLZ · Semaphorin 4D: “The ligand-binding face of the semaphorins revealed by the high resolution crystal structure of SEMA4D”. X-ray diffraction, 14 pockets (best druggability 0.75). MolNFT v1 #17203 on GenesisL1: 3D structure, binding…
- PDB
- 1OLZ
- Type
- protein
- Length
- 1,242 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Semaphorin 4D
- UniProt
- Q92854
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Semaphorin 4D | protein | 621 | 10% helix, 41% strand | Q92854 |
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.75 | 0.78 | 72 | empty |
| 2 | 1033 | 0.75 | 0.77 | 83 | empty |
| 3 | 358 | 0.57 | 0.75 | 46 | empty |
| 4 | 118 | 0.51 | 0.81 | 24 | empty |
| 5 | 120 | 0.50 | 0.80 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1555 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 1OLZ · The ligand-binding face of the semaphorins revealed by the high resolution crystal… · the same entry in another collection · chain A against A, TM-score 1.00
- Q92854 · AlphaFold monomer V2.0 prediction for semaphorin-4D (Q92854) · a predicted model of the same protein · chain A 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 Q92854
- Elsewhere: RCSB PDB 1OLZ · PDBe 1OLZ · UniProt Q92854
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