MolNFT v1 · #48019 · protein

Inhibitor-free human thrombin mutant C191A-C220A

2PGB · Prothrombin: “Inhibitor-free human thrombin mutant C191A-C220A”. X-ray diffraction, 2 ligands (NAG, SO4), 2 pockets (best druggability 0.56). MolNFT v1 #48019 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2PGB
Type: protein
Length: 289 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prothrombin
EC: 3.4.21.5
UniProt: P00734
Ligands: NAG, SO4
Pockets: 2 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 17% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Prothrombin (EC 3.4.21.5)	protein	35	37% helix, 0% strand	P00734
B	Prothrombin (EC 3.4.21.5)	protein	254	14% helix, 34% strand	P00734

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
SO4 · Sulfate ion · ion · 2 copies · chains B

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

Pockets

2 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	255	0.56	0.77	37	empty
2	61	0.33	0.76	13	empty

Interfaces

1 interface between chains.

A–B · 1407 Å² buried · 36 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

2PGB · Inhibitor-free human thrombin mutant C191A-C220A · 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 2PGB · PDBe 2PGB · UniProt P00734

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