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Crystal structure of human prethrombin-1

Analyse Crystal structure of human prethrombin-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3NXP
Type: protein
Length: 388 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prethrombin-1
EC: 3.4.21.5
UniProt: P00734
Ligands: NAG
Pockets: 5 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 16% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Prethrombin-1 (EC 3.4.21.5)	protein	388	16% helix, 25% strand	P00734

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A
GOL · Glycerol · additive · 2 copies · chains A

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

Pockets

5 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	176	0.54	0.80	24	empty
2	152	0.44	0.75	24	GOL
3	113	0.37	0.73	22	empty
4	80	0.35	0.76	23	empty
5	62	0.35	0.77	14	empty

Modifications

Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

3NXP · Crystal structure of human prethrombin-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 P00734
Elsewhere: RCSB PDB 3NXP · PDBe 3NXP · UniProt P00734

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