MolNFT v1 · #86680 · protein

Crystal structure of a truncated B-domain human factor VIII

4BDV · Factor viiia heavy chain, 92 kda isoform, B domain: “Crystal structure of a truncated B-domain human factor VIII”. X-ray diffraction, 5 ligands (NAG, BMA, ZN), 17 pockets (best druggability 0.87). MolNFT v1 #86680 on GenesisL1: 3D…

PDB: 4BDV
Type: protein
Length: 1,218 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Factor viiia heavy chain, 92 kda isoform, B domain; Factor viiia light chain
UniProt: P00451
Ligands: NAG, BMA, ZN, CA, CU1
Pockets: 17 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Factor viiia heavy chain, 92 kda isoform, B domain	protein	612	6% helix, 35% strand	P00451
B	Factor viiia light chain	protein	606	3% helix, 42% strand	P00451

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 3 copies · chains B
ZN · Zinc ion · metal · chains A
CA · Calcium ion · metal · chains A
CU1 · Copper (I) ion · metal · chains B
EDO · 1,2-ethanediol · additive · 2 copies · chains A, B

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

Pockets

17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	608	0.87	0.91	55	EDO
2	1038	0.78	0.80	81	NAG, EDO
3	537	0.69	0.79	54	empty
4	279	0.65	0.81	42	empty
5	459	0.64	0.77	48	empty

Interfaces

1 interface between chains.

A–B · 3673 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

4BDV · Crystal structure of a truncated B-domain human factor VIII · the same entry in another collection · chain A against A, TM-score 1.00
P00451 · AlphaFold monomer V2.0 prediction for coagulation factor VIII (P00451) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P00451
Elsewhere: RCSB PDB 4BDV · PDBe 4BDV · UniProt P00451

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