MolNFT v1 · #121644 · protein

Crystal structure of human germline antibody IGHV3-53/IGKV4-1

5I1I · Fab light chain: “Crystal structure of human germline antibody IGHV3-53/IGKV4-1”. X-ray diffraction, 3 pockets (best druggability 0.56). MolNFT v1 #121644 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5I1I
Type: protein
Length: 428 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab light chain; Fab heavy chain
Pockets: 3 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab light chain	protein	219	4% helix, 52% strand	—
H	Fab heavy chain	protein	209	7% helix, 48% strand	—

Pockets

3 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	392	0.56	0.74	46	empty
2	75	0.34	0.75	25	empty
3	74	0.29	0.72	18	empty

Interfaces

1 interface between chains.

L–H · 1662 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5I1I · Crystal structure of human germline antibody IGHV3-53/IGKV4-1 · 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 5I1I · PDBe 5I1I

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