MolNFT v1 · #139806 · protein

Structure of monomeric mutant of rei immunoglobulin light chain variable domain crystallized at pH 8

5XQY · Immunoglobulin kappa variable 1D-33: “Structure of monomeric mutant of rei immunoglobulin light chain variable domain crystallized at pH 8”. X-ray diffraction, 3 pockets (best druggability 0.70). MolNFT v1 #139806 on GenesisL1: 3D…

PDB: 5XQY
Type: protein
Length: 872 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Immunoglobulin kappa variable 1D-33
Pockets: 3 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Immunoglobulin kappa variable 1D-33	protein	109	3% helix, 50% strand	—

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	823	0.70	0.76	60	empty
2	139	0.54	0.81	26	empty
3	112	0.51	0.82	25	empty

Interfaces

10 interfaces between chains.

B–C · 483 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 463 Å² buried · 8 hydrogen bonds · protein-protein
F–H · 416 Å² buried · 8 hydrogen bonds · protein-protein
E–G · 409 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 259 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5XQY · Structure of monomeric mutant of REI immunoglobulin light chain variable domain… · 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 5XQY · PDBe 5XQY

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