MolNFT v1 · #47300 · protein
Crystal structure of the thrombospondin-1 N-terminal domain in complex with fractionated heparin DP10
2OUH: “Crystal structure of the thrombospondin-1 N-terminal domain in complex with fractionated heparin DP10”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.60). MolNFT v1 #47300 on GenesisL1: 3D structure, binding…
- PDB
- 2OUH
- Type
- protein
- Length
- 406 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombospondin-1
- UniProt
- P07996
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thrombospondin-1 | protein | 203 | 19% helix, 42% strand | P07996 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.60 | 0.76 | 45 | empty |
| 2 | 137 | 0.47 | 0.78 | 19 | empty |
| 3 | 67 | 0.35 | 0.77 | 18 | empty |
| 4 | 50 | 0.27 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 293 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2OUH · Crystal structure of the Thrombospondin-1 N-terminal domain in complex with fractionated… · the same entry in another collection · chain A against A, TM-score 1.00
- P07996 · AlphaFold monomer V2.0 prediction for thrombospondin-1 (P07996) · a predicted model of the same protein · chain A 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 P07996
- Elsewhere: RCSB PDB 2OUH · PDBe 2OUH · UniProt P07996
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