MolNFT v1 · #11823 · protein

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

1JY2 · 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 #11823 on GenesisL1: 3D structure…

PDB: 1JY2
Type: protein
Length: 278 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 · 5 distinct chains · 58% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
N, Q	Fibrinogen alpha chain	protein	43	67% helix, 12% strand	—
O	Fibrinogen beta chain	protein	51	53% helix, 12% strand	P02676
P	Fibrinogen gamma-B chain	protein	44	59% helix, 11% strand	P12799
R	Fibrinogen beta chain	protein	50	52% helix, 12% strand	P02676
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	38	empty
2	93	0.36	0.74	14	empty
3	91	0.36	0.75	15	empty

Interfaces

14 interfaces between chains.

Q–R · 921 Å² buried · 10 hydrogen bonds · protein-protein
N–O · 902 Å² buried · 11 hydrogen bonds · protein-protein
Q–S · 781 Å² buried · 10 hydrogen bonds · protein-protein
O–P · 780 Å² buried · 7 hydrogen bonds · protein-protein
N–P · 772 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

1JY2 · Crystal Structure of the Central Region of Bovine Fibrinogen (E5 fragment) at 1.4… · the same entry in another collection · chain P against P, TM-score 1.00
P02676 · AlphaFold monomer V2.0 prediction for fibrinogen beta chain (P02676) · a predicted model of the same protein · chain R against A, TM-score 0.84
P12799 · AlphaFold monomer V2.0 prediction for fibrinogen gamma-B chain (P12799) · a predicted model of the same protein · chain P against A, TM-score 0.78

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 1JY2 · PDBe 1JY2 · UniProt P02676 · UniProt P12799

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