MolNFT v1 · #139343 · protein

Crystal structure of TS2/16 fv-clasp fragment

5XCX · VH(S112C)-sarah chimera: “Crystal structure of TS2/16 fv-clasp fragment”. X-ray diffraction, 1 ligand (PO4), 3 pockets (best druggability 0.61). MolNFT v1 #139343 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XCX
Type: protein
Length: 331 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VH(S112C)-sarah chimera; Vl-SARAH(S37C) chimera
Ligands: PO4
Pockets: 3 · best druggability 0.61

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VH(S112C)-sarah chimera	protein	171	30% helix, 36% strand	—
B	Vl-SARAH(S37C) chimera	protein	160	30% helix, 38% strand	—

Ligands and binding sites

PO4 · Phosphate ion · ion · 3 copies · chains A, B
CXS · 3-cyclohexyl-1-propylsulfonic acid · additive · 2 copies · chains A, B
GOL · Glycerol · additive · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	363	0.61	0.78	52	empty
2	236	0.54	0.77	39	PO4, GOL
3	90	0.39	0.77	18	empty

Interfaces

1 interface between chains.

A–B · 2714 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5XCX · Crystal structure of TS2/16 Fv-clasp fragment · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 5XCX · PDBe 5XCX

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