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Crystal structure of the mouse mab 17.2

Analyse Crystal structure of the mouse mab 17.2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3SGD
Type: protein
Length: 869 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Light chain; Heavy chain
Ligands: CA
Pockets: 11 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, I	Light chain	protein	218	6% helix, 51% strand	—
H	Heavy chain	protein	217	10% helix, 52% strand	—
J	Heavy chain	protein	216	7% helix, 50% strand	—

Ligands and binding sites

CA · Calcium ion · metal · 3 copies · chains L, H, I

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

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1134	0.77	0.79	112	empty
2	702	0.65	0.75	72	empty
3	454	0.60	0.75	52	CA
4	221	0.53	0.77	35	empty
5	156	0.49	0.78	32	empty

Interfaces

5 interfaces between chains.

L–H · 1774 Å² buried · 12 hydrogen bonds · protein-protein
I–J · 1672 Å² buried · 14 hydrogen bonds · protein-protein
L–J · 569 Å² buried · 13 hydrogen bonds · protein-protein
L–I · 90 Å² buried · 0 hydrogen bonds · protein-protein
H–J · 39 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

3SGD · Crystal structure of the mouse mAb 17.2 · the same entry in another collection · chain L against L, 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
Elsewhere: RCSB PDB 3SGD · PDBe 3SGD

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