MolNFT v1 · #144114 · protein

Crystal structure of prothrombin mutant S101C/A470C

6BJR: “Crystal structure of prothrombin mutant S101C/A470C”. X-ray diffraction, 3 ligands (NAG, BMA, MG), 16 pockets (best druggability 0.87). MolNFT v1 #144114 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6BJR
Type: protein
Length: 575 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prothrombin
EC: 3.4.21.5
UniProt: P00734
Ligands: NAG, BMA, MG
Pockets: 16 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 15% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Prothrombin (EC 3.4.21.5)	protein	575	15% helix, 12% strand	P00734

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
BMA · beta-D-mannopyranose · sugar
MG · Magnesium ion · metal · 6 copies · chains A

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

Pockets

16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	515	0.87	0.93	41	empty
2	450	0.77	0.85	51	empty
3	149	0.76	0.94	27	empty
4	420	0.75	0.84	65	empty
5	441	0.74	0.83	48	empty

Modifications

Observed in the structure: 13 disulfide, 10 modified, 2 glycan (disulfide, carboxylation, N-glycosylation).

Compared structures

6BJR · Crystal structure of prothrombin mutant S101C/A470C · 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 6BJR · PDBe 6BJR · UniProt P00734

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