Research workbench

Hapc-C25K23 Fab complex

Analyse Hapc-C25K23 Fab complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6M3B
Type: protein
Length: 756 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vitamin K-dependent protein C heavy chain; Vitamin K-dependent protein C light chain…
EC: 3.4.21.69
UniProt: P04070
Ligands: NAG
Pockets: 9 · best druggability 0.58

Structure

x-ray diffraction · 4 distinct chains · 9% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vitamin K-dependent protein C heavy chain (EC 3.4.21.69)	protein	228	14% helix, 37% strand	P04070
D	Vitamin K-dependent protein C light chain (EC 3.4.21.69)	protein	91	4% helix, 26% strand	P04070
B	C25K23 Fab L chain	protein	214	7% helix, 50% strand	—
C	C25K23 Fab H chain	protein	223	7% helix, 46% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, D

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

Pockets

9 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	273	0.58	0.78	40	empty
2	294	0.53	0.75	47	empty
3	282	0.52	0.75	37	empty
4	50	0.41	0.82	14	empty
5	107	0.41	0.76	22	empty

Interfaces

4 interfaces between chains.

B–C · 1860 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 816 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 814 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 93 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 15 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

6M3B · hAPC-c25k23 Fab complex · the same entry in another collection · chain A against A, TM-score 1.00
P04070 · AlphaFold monomer V2.0 prediction for vitamin K-dependent protein C (P04070) · a predicted model of the same protein · chain A 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 P04070
Elsewhere: RCSB PDB 6M3B · PDBe 6M3B · UniProt P04070

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