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Crystal structure of celd in complex with affitin E12

Analyse Crystal structure of celd in complex with affitin E12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4CJ0
Type: protein
Length: 594 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endoglucanase D; E12 affitin
EC: 3.2.1.4
UniProt: P0C2S4
Ligands: CA, ZN
Pockets: 5 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Endoglucanase D (EC 3.2.1.4)	protein	534	39% helix, 15% strand	P0C2S4
B	E12 affitin	protein	60	27% helix, 53% strand	—

Ligands and binding sites

CA · Calcium ion · metal · 3 copies · chains A
ZN · Zinc ion · metal · chains A
GOL · Glycerol · additive · 6 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	174	0.56	0.81	33	GOL
2	97	0.38	0.75	18	GOL
3	86	0.35	0.75	16	empty
4	65	0.34	0.77	15	empty
5	52	0.30	0.76	18	empty

Interfaces

1 interface between chains.

A–B · 701 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4CJ0 · Crystal structure of CelD in complex with affitin E12 · the same entry in another collection · chain A against A, TM-score 1.00
P0C2S4 · AlphaFold monomer V2.0 prediction for endoglucanase D (P0C2S4) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P0C2S4
Elsewhere: RCSB PDB 4CJ0 · PDBe 4CJ0 · UniProt P0C2S4

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