MolNFT v1 · #15557 · protein

Fragment double-D from human fibrin

1N8E · Fibrin ALPHA/ALPHA-E chain: “Fragment double-D from human fibrin”. X-ray diffraction, 3 pockets (best druggability 0.40). MolNFT v1 #15557 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1N8E
Type: protein
Length: 1,352 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fibrin ALPHA/ALPHA-E chain; Fibrin beta chain; Fibrin gamma chain
UniProt: P02671, P02675, P02679
Pockets: 3 · best druggability 0.40

Structure

x-ray diffraction · 3 distinct chains · 0% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Fibrin ALPHA/ALPHA-E chain	protein	74	0% helix, 0% strand	P02671
B, E	Fibrin beta chain	protein	307	0% helix, 0% strand	P02675
C, F	Fibrin gamma chain	protein	295	0% helix, 0% strand	P02679

Pockets

3 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	124	0.40	0.73	34	empty
2	74	0.32	0.72	27	empty
3	58	0.29	0.72	16	empty

Interfaces

7 interfaces between chains.

E–F · 241 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 230 Å² buried · 0 hydrogen bonds · protein-protein
D–E · 223 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 190 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 37 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1N8E · Fragment Double-D from Human Fibrin · the same entry in another collection · chain F against F, TM-score 1.00
P02675 · AlphaFold monomer V2.0 prediction for fibrinogen beta chain (P02675) · a predicted model of the same protein · chain B 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 0.98
P02671 · AlphaFold monomer V2.0 prediction for fibrinogen alpha chain (P02671) · a predicted model of the same protein · chain A against A, TM-score 0.87

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 1N8E · PDBe 1N8E · UniProt P02671 · UniProt P02675 · UniProt P02679

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