MolNFT v1 · #28387 · protein

The crystal structure of fibrinogen-aa peptide 1-23 (F8Y) bound to bovine thrombin explains why the mutation of phe-8 to tyrosine strongly inhibits normal cleavage at arginine-16

1YCP · Epsilon thrombin: “The crystal structure of fibrinogen-aa peptide 1-23 (F8Y) bound to bovine thrombin explains why the mutation…”. X-ray diffraction, 6 pockets (best druggability 0.42). MolNFT v1 #28387 on GenesisL1: 3D structure…

PDB: 1YCP
Type: protein
Length: 564 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Epsilon thrombin; Alpha thrombin; Fibrinopeptide a-alpha
EC: 3.4.21.5
UniProt: P00735, P02671
Pockets: 6 · best druggability 0.42

Structure

x-ray diffraction · 5 distinct chains · 15% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, J	Epsilon thrombin (EC 3.4.21.5)	protein	29	31% helix, 0% strand	P00735
H	Alpha thrombin (EC 3.4.21.5)	protein	247	15% helix, 36% strand	P00735
F, N	Fibrinopeptide a-alpha	protein	6	0% helix, 17% strand	P02671
K	Epsilon thrombin	protein	146	12% helix, 35% strand	P00735
M	Epsilon thrombin	protein	101	16% helix, 32% strand	P00735

Pockets

6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	53	0.42	0.83	15	empty
2	88	0.42	0.78	17	empty
3	172	0.41	0.73	22	empty
4	74	0.37	0.77	17	empty
5	103	0.33	0.72	11	empty

Interfaces

8 interfaces between chains.

K–M · 3278 Å² buried · 51 hydrogen bonds · protein-protein
L–H · 1160 Å² buried · 19 hydrogen bonds · protein-protein
J–K · 844 Å² buried · 12 hydrogen bonds · protein-protein
H–F · 610 Å² buried · 19 hydrogen bonds · protein-protein
J–M · 564 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

1YCP · The crystal structure of fibrinogen-aa peptide 1-23 (F8Y) bound to bovine thrombin… · the same entry in another collection · chain M against M, TM-score 1.00
P02671 · AlphaFold monomer V2.0 prediction for fibrinogen alpha chain (P02671) · a predicted model of the same protein · chain F against A, TM-score 0.62

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 P00735
Every structure of UniProt P02671
Elsewhere: RCSB PDB 1YCP · PDBe 1YCP · UniProt P00735 · UniProt P02671

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