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Crystal structure of SAG506-01, tetragonal, crystal 2

Analyse Crystal structure of SAG506-01, tetragonal, crystal 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3DV6
Type: protein
Length: 233 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antibody fv fragment SAG506-01; Ig-like protein
Ligands: KDO, MG
Pockets: 2 · best druggability 0.30

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Antibody fv fragment SAG506-01	protein	112	3% helix, 54% strand	—
B	Ig-like protein	protein	121	7% helix, 50% strand	—

Ligands and binding sites

KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A
PG4 · Tetraethylene glycol · additive · chains B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	79	0.30	0.73	17	empty
2	52	0.23	0.71	13	empty

Interfaces

1 interface between chains.

A–B · 841 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

3DV6 · Crystal structure of SAG506-01, tetragonal, crystal 2 · the same entry in another collection · 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
Elsewhere: RCSB PDB 3DV6 · PDBe 3DV6

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