Research workbench

Anti-fixa Fab of MIM8 in complex with human fixa

Analyse Anti-fixa Fab of MIM8 in complex with human fixa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7AHV
Type: protein
Length: 726 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anti-fixa Fab of MIM8 heavy chain; Anti-fixa Fab of MIM8 light chain; Coagulation factor…
EC: 3.4.21.22
UniProt: P00740
Ligands: 0GJ, CA, SO4
Pockets: 8 · best druggability 0.60

Structure

x-ray diffraction · 4 distinct chains · 10% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Anti-fixa Fab of MIM8 heavy chain	protein	223	9% helix, 50% strand	—
B	Anti-fixa Fab of MIM8 light chain	protein	214	6% helix, 51% strand	—
L	Coagulation factor IX (EC 3.4.21.22)	protein	54	13% helix, 26% strand	P00740
H	Coagulation factor IX (EC 3.4.21.22)	protein	235	13% helix, 36% strand	P00740

Ligands and binding sites

0GJ · L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide · ligand · chains H
CA · Calcium ion · metal · chains H
SO4 · Sulfate ion · ion · 17 copies · chains A, B, H, L

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	511	0.60	0.74	50	empty
2	206	0.55	0.78	25	SO4
3	85	0.52	0.84	17	empty
4	133	0.42	0.75	22	SO4
5	72	0.36	0.76	15	empty

Interfaces

4 interfaces between chains.

A–B · 1980 Å² buried · 17 hydrogen bonds · protein-protein
L–H · 740 Å² buried · 7 hydrogen bonds · protein-protein
A–H · 417 Å² buried · 6 hydrogen bonds · protein-protein
B–H · 179 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

7AHV · Anti-FIXa Fab of mim8 in complex with human FIXa · the same entry in another collection · chain A against A, TM-score 1.00
P00740 · AlphaFold monomer V2.0 prediction for coagulation factor IX (P00740) · a predicted model of the same protein · chain H 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 P00740
Elsewhere: RCSB PDB 7AHV · PDBe 7AHV · UniProt P00740

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