MolNFT v1 · #11824 · protein

Crystal structure of the central region of bovine fibrinogen (E5 fragment) at 1.4 ångströms resolution

1JY3 · Fibrinogen alpha chain: “Crystal structure of the central region of bovine fibrinogen (E5 fragment) at 1.4 ångströms resolution”. X-ray diffraction, 3 pockets (best druggability 0.71). MolNFT v1 #11824 on GenesisL1: 3D structure…

PDB: 1JY3
Type: protein
Length: 283 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fibrinogen alpha chain; Fibrinogen beta chain; Fibrinogen gamma-B chain
UniProt: P02676, P12799
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 4 distinct chains · 58% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
N, Q	Fibrinogen alpha chain	protein	44	68% helix, 9% strand	—
O, R	Fibrinogen beta chain	protein	51	53% helix, 12% strand	P02676
P	Fibrinogen gamma-B chain	protein	46	50% helix, 17% strand	P12799
S	Fibrinogen gamma-B chain	protein	47	62% helix, 6% strand	P12799

Pockets

3 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	259	0.71	0.86	39	empty
2	103	0.40	0.76	17	empty
3	66	0.28	0.73	14	empty

Interfaces

14 interfaces between chains.

Q–R · 902 Å² buried · 9 hydrogen bonds · protein-protein
N–O · 880 Å² buried · 10 hydrogen bonds · protein-protein
Q–S · 776 Å² buried · 9 hydrogen bonds · protein-protein
P–S · 764 Å² buried · 5 hydrogen bonds · protein-protein
O–P · 758 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

1JY3 · Crystal Structure of the Central Region of Bovine Fibrinogen (E5 Fragment) at 1.4… · the same entry in another collection · chain S against S, TM-score 1.00
P02676 · AlphaFold monomer V2.0 prediction for fibrinogen beta chain (P02676) · a predicted model of the same protein · chain O against A, TM-score 0.82
P12799 · AlphaFold monomer V2.0 prediction for fibrinogen gamma-B chain (P12799) · a predicted model of the same protein · chain S against A, TM-score 0.75

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 P02676
Every structure of UniProt P12799
Elsewhere: RCSB PDB 1JY3 · PDBe 1JY3 · UniProt P02676 · UniProt P12799

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