MolNFT v1 · #166940 · protein

Crystal structure of human prethrombin-2 with tryptophans replaced by 5-F-tryptophan

6V5T · Prothrombin: “Crystal structure of human prethrombin-2 with tryptophans replaced by 5-F-tryptophan”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.70). MolNFT v1 #166940 on GenesisL1: 3D structure, binding sites…

PDB: 6V5T
Type: protein
Length: 290 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: SO4
Pockets: 4 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 18% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Prothrombin (EC 3.4.21.5)	protein	290	18% helix, 29% strand	P00734

Ligands and binding sites

SO4 · Sulfate ion · ion · chains E
GOL · Glycerol · additive · chains E

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	114	0.70	0.92	30	empty
2	101	0.54	0.84	27	GOL
3	112	0.39	0.75	21	empty
4	55	0.33	0.77	13	empty

Modifications

Observed in the structure: 9 modified, 4 disulfide (nonstandard, disulfide).

Compared structures

6V5T · Crystal structure of human prethrombin-2 with tryptophans replaced by 5-F-tryptophan · the same entry in another collection · chain E against E, 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 6V5T · PDBe 6V5T · UniProt P00734

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