MolNFT v1 · #47436 · protein

Crystal structure of fragment D of GAMMAD298,301A fibrinogen with the peptide ligand gly-pro-arg-pro-amide

2OYI · Fibrinogen alpha chain: “Crystal structure of fragment D of GAMMAD298,301A fibrinogen with the peptide ligand gly-pro-arg-pro-amide”. X-ray diffraction, 3 ligands (NAG, FUC, CA), 14 pockets (best druggability 0.61). MolNFT v1 #47436…

PDB: 2OYI
Type: protein
Length: 1,316 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fibrinogen alpha chain; Fibrinogen beta chain; Fibrinogen gamma chain; Gprp peptide
UniProt: P02671, P02675, P02679
Ligands: NAG, FUC, CA
Pockets: 14 · best druggability 0.61

Structure

x-ray diffraction · 7 distinct chains · 27% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fibrinogen alpha chain	protein	65	71% helix, 2% strand	P02671
B	Fibrinogen beta chain	protein	301	25% helix, 26% strand	P02675
C	Fibrinogen gamma chain	protein	299	23% helix, 24% strand	P02679
D	Fibrinogen alpha chain	protein	56	61% helix, 2% strand	P02671
E	Fibrinogen beta chain	protein	294	22% helix, 27% strand	P02675
F	Fibrinogen gamma chain	protein	285	21% helix, 27% strand	P02679
G, H, I, J	Gprp peptide	protein	4	0% helix, 0% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, H, E, J
FUC · alpha-L-fucopyranose · sugar · 2 copies · chains B, E, J
CA · Calcium ion · metal · 4 copies · chains B, C, E, F

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

Pockets

14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	166	0.61	0.83	28	empty
2	197	0.60	0.81	33	empty
3	158	0.60	0.83	26	empty
4	201	0.59	0.81	35	empty
5	314	0.57	0.76	36	empty

Interfaces

10 interfaces between chains.

B–C · 2198 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 1922 Å² buried · 27 hydrogen bonds · protein-protein
E–F · 1921 Å² buried · 19 hydrogen bonds · protein-protein
D–E · 1696 Å² buried · 25 hydrogen bonds · protein-protein
A–C · 872 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

2OYI · Crystal Structure of Fragment D of gammaD298,301A Fibrinogen with the Peptide Ligand… · the same entry in another collection · chain J against J, TM-score 1.00
P02675 · AlphaFold monomer V2.0 prediction for fibrinogen beta chain (P02675) · a predicted model of the same protein · chain E against A, TM-score 0.99

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 P02671
Every structure of UniProt P02675
Every structure of UniProt P02679
Elsewhere: RCSB PDB 2OYI · PDBe 2OYI · UniProt P02671 · UniProt P02675 · UniProt P02679

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.