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The CA+2 ion and membrane binding structure of the gla domain of ca- prothrombin fragment 1

Analyse The CA+2 ion and membrane binding structure of the gla domain of ca… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2PF2
Type: protein
Length: 145 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prothrombin fragment 1
UniProt: P00735
Ligands: CA
Pockets: 1 · best druggability 0.28

Structure

x-ray diffraction · 1 distinct chain · 23% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Prothrombin fragment 1	protein	145	23% helix, 10% strand	P00735

Ligands and binding sites

CA · Calcium ion · metal · 7 copies · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	51	0.28	0.75	14	empty

Modifications

Observed in the structure: 10 modified, 5 disulfide (carboxylation, disulfide).

Compared structures

2PF2 · The CA+2 ion and membrane binding structure of the gla domain of ca-prothrombin fragment 1 · 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
Every structure of UniProt P00735
Elsewhere: RCSB PDB 2PF2 · PDBe 2PF2 · UniProt P00735

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