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Crystal structure of ergic-53/MCFD2, monoclinic calcium-bound form 1

Analyse Crystal structure of ergic-53/MCFD2, monoclinic calcium-bound form 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YGC
Type: protein
Length: 1,151 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein ergic-53; Multiple coagulation factor deficiency protein 2
UniProt: P49257, Q8NI22
Ligands: CA, CL
Pockets: 14 · best druggability 0.70

Structure

x-ray diffraction · 6 distinct chains · 22% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein ergic-53	protein	228	3% helix, 47% strand	P49257
B	Multiple coagulation factor deficiency protein 2	protein	64	59% helix, 6% strand	Q8NI22
C, E, G	Protein ergic-53	protein	227	3% helix, 47% strand	P49257
D	Multiple coagulation factor deficiency protein 2	protein	66	59% helix, 6% strand	Q8NI22
F	Multiple coagulation factor deficiency protein 2	protein	54	56% helix, 4% strand	Q8NI22
H	Multiple coagulation factor deficiency protein 2	protein	58	59% helix, 7% strand	Q8NI22

Ligands and binding sites

CA · Calcium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
CL · Chloride ion · ion · 4 copies · chains A, B, C, D, E, F, G, H

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

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	685	0.70	0.77	56	CL
2	571	0.68	0.77	41	empty
3	350	0.59	0.76	35	empty
4	102	0.56	0.85	22	CL
5	200	0.55	0.79	39	CL

Interfaces

9 interfaces between chains.

E–F · 803 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 773 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 760 Å² buried · 10 hydrogen bonds · protein-protein
G–H · 738 Å² buried · 11 hydrogen bonds · protein-protein
A–H · 383 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4YGC · Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-bound form 1 · the same entry in another collection · chain G against G, TM-score 1.00
P49257 · AlphaFold monomer V2.0 prediction for protein ergic-53 (P49257) · a predicted model of the same protein · chain C against A, TM-score 1.00
Q8NI22 · AlphaFold monomer V2.0 prediction for multiple coagulation factor deficiency protein 2… · 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 P49257
Every structure of UniProt Q8NI22
Elsewhere: RCSB PDB 4YGC · PDBe 4YGC · UniProt P49257 · UniProt Q8NI22

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