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Crystal structure of thrombospondin-1 N-terminal domain in P1 form at 1.85A resolution

Analyse Crystal structure of thrombospondin-1 N-terminal domain in P1 form at 1.85A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ES3
Type: protein
Length: 417 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thrombospondin-1
UniProt: P07996
Pockets: 3 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 18% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thrombospondin-1	protein	209	19% helix, 43% strand	P07996
B	Thrombospondin-1	protein	208	17% helix, 43% strand	P07996

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	293	0.62	0.80	43	empty
2	188	0.50	0.77	33	empty
3	84	0.42	0.79	19	empty

Interfaces

1 interface between chains.

A–B · 533 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

2ES3 · Crystal Structure of Thrombospondin-1 N-terminal Domain in P1 Form at 1.85A Resolution · 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 B 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 P07996
Elsewhere: RCSB PDB 2ES3 · PDBe 2ES3 · UniProt P07996

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