MolNFT v1 · #78385 · protein

Structure of thrombin mutant Y225P in the E* form

3S7H · Prothrombin: “Structure of thrombin mutant Y225P in the E* form”. X-ray diffraction, 1 ligand (NAG), 2 pockets (best druggability 0.55). MolNFT v1 #78385 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3S7H
Type: protein
Length: 275 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
Pockets: 2 · best druggability 0.55

Structure

x-ray diffraction · 2 distinct chains · 16% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Prothrombin (EC 3.4.21.5)	protein	27	37% helix, 0% strand	P00734
B	Prothrombin (EC 3.4.21.5)	protein	248	13% helix, 33% strand	P00734

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
GOL · Glycerol · additive · 2 copies · chains A, 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	173	0.55	0.80	28	empty
2	73	0.36	0.77	19	empty

Interfaces

1 interface between chains.

A–B · 1143 Å² buried · 27 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

3S7H · Structure of thrombin mutant Y225P in the E* form · 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 3S7H · PDBe 3S7H · UniProt P00734

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