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Crystal structure of human germline antibody IGHV5-51/IGKV3-11

Analyse Crystal structure of human germline antibody IGHV5-51/IGKV3-11 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5I1J
Type: protein
Length: 427 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab light chain; Fab heavy chain
Pockets: 4 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab light chain	protein	214	6% helix, 50% strand	—
H	Fab heavy chain	protein	213	9% helix, 52% strand	—

Ligands and binding sites

GOL · Glycerol · additive · chains L, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	399	0.58	0.75	44	empty
2	212	0.50	0.76	36	empty
3	89	0.40	0.77	21	empty
4	92	0.34	0.74	22	empty

Interfaces

1 interface between chains.

L–H · 1701 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

5I1J · Crystal structure of human germline antibody IGHV5-51/IGKV3-11 · 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 5I1J · PDBe 5I1J

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