MolNFT v1 · #111091 · protein

Crystal structure of ergic-53/MCFD2, monoclinic calcium-bound form 2

4YGD · Protein ergic-53: “Crystal structure of ergic-53/MCFD2, monoclinic calcium-bound form 2”. X-ray diffraction, 2 ligands (CA, CL), 13 pockets (best druggability 0.66). MolNFT v1 #111091 on GenesisL1: 3D structure, binding sites and…

PDB: 4YGD
Type: protein
Length: 1,172 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: 13 · best druggability 0.66

Structure

x-ray diffraction · 5 distinct chains · 33% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Protein ergic-53	protein	227	3% helix, 46% strand	P49257
B	Multiple coagulation factor deficiency protein 2	protein	69	61% helix, 6% strand	Q8NI22
D	Multiple coagulation factor deficiency protein 2	protein	62	56% helix, 6% strand	Q8NI22
F	Multiple coagulation factor deficiency protein 2	protein	63	57% helix, 6% strand	Q8NI22
H	Multiple coagulation factor deficiency protein 2	protein	70	60% helix, 6% 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 · 3 copies · chains A, B, G, H

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

Pockets

13 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	526	0.66	0.77	65	empty
2	407	0.60	0.76	54	empty
3	433	0.59	0.75	54	empty
4	275	0.58	0.78	43	empty
5	96	0.54	0.84	24	CL

Interfaces

7 interfaces between chains.

A–B · 840 Å² buried · 10 hydrogen bonds · protein-protein
G–H · 839 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 768 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 743 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 645 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4YGD · Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-bound form 2 · the same entry in another collection · chain H against H, TM-score 1.00
P49257 · AlphaFold monomer V2.0 prediction for protein ergic-53 (P49257) · a predicted model of the same protein · chain A 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 D against A, TM-score 0.95

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 4YGD · PDBe 4YGD · UniProt P49257 · UniProt Q8NI22

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