MolNFT v1 · #7185 · protein

Crystal structure of crosslinked fragment D

1FZB · Fibrinogen: “Crystal structure of crosslinked fragment D”. X-ray diffraction, 2 ligands (NAG, CA), 19 pockets (best druggability 0.69). MolNFT v1 #7185 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1FZB
Type: protein
Length: 1,414 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fibrinogen; Peptide ligand gprg
UniProt: P02671, P02675, P02679
Ligands: NAG, CA
Pockets: 19 · best druggability 0.69

Structure

x-ray diffraction · 5 distinct chains · 27% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Fibrinogen	protein	81	68% helix, 1% strand	P02671
B, E	Fibrinogen	protein	312	24% helix, 24% strand	P02675
C	Fibrinogen	protein	309	23% helix, 23% strand	P02679
F	Fibrinogen	protein	311	25% helix, 24% strand	P02679
G, H	Peptide ligand gprg	protein	4	0% helix, 0% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, E
CA · Calcium ion · metal · 2 copies · chains C, F

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

Pockets

19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	485	0.69	0.79	38	empty
2	186	0.69	0.87	36	empty
3	136	0.66	0.88	28	empty
4	131	0.62	0.86	27	empty
5	124	0.59	0.85	27	empty

Interfaces

9 interfaces between chains.

B–C · 2210 Å² buried · 25 hydrogen bonds · protein-protein
D–E · 2067 Å² buried · 27 hydrogen bonds · protein-protein
E–F · 1993 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1924 Å² buried · 26 hydrogen bonds · protein-protein
D–F · 1078 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

1FZB · Crystal structure of crosslinked fragment D · the same entry in another collection · chain H against H, 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 0.98
P02679 · AlphaFold monomer V2.0 prediction for fibrinogen gamma chain (P02679) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 1FZB · PDBe 1FZB · UniProt P02671 · UniProt P02675 · UniProt P02679

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