MolNFT v1 · #68776 · protein

Crystal structure of prethombin-2/FRAGMENT-2 complex

3K65 · Prothrombin: “Crystal structure of prethombin-2/FRAGMENT-2 complex”. X-ray diffraction, 5 pockets (best druggability 0.54). MolNFT v1 #68776 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3K65
Type: protein
Length: 354 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prothrombin
EC: 3.4.21.5
UniProt: P00734
Pockets: 5 · best druggability 0.54

Structure

x-ray diffraction · 2 distinct chains · 16% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Prothrombin (EC 3.4.21.5)	protein	80	13% helix, 14% strand	P00734
B	Prothrombin (EC 3.4.21.5)	protein	274	16% helix, 32% strand	P00734

Ligands and binding sites

BU1 · 1,4-butanediol · additive · 2 copies · chains A, B

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	131	0.54	0.82	22	empty
2	148	0.47	0.77	23	BU1
3	99	0.42	0.77	24	empty
4	82	0.37	0.77	17	empty
5	50	0.35	0.79	16	empty

Interfaces

1 interface between chains.

A–B · 834 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3K65 · Crystal Structure of Prethombin-2/Fragment-2 Complex · 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 3K65 · PDBe 3K65 · UniProt P00734

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