MolNFT v1 · #121638 · protein

Crystal structure of human germline antibody IGHV3-23/IGKV3-20

5I1C · Fab light chain: “Crystal structure of human germline antibody IGHV3-23/IGKV3-20”. X-ray diffraction, 1 ligand (CL), 5 pockets (best druggability 0.56). MolNFT v1 #121638 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5I1C
Type: protein
Length: 430 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab light chain; Fab heavy chain
Ligands: CL
Pockets: 5 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab light chain	protein	215	7% helix, 50% strand	—
H	Fab heavy chain	protein	215	8% helix, 52% strand	—

Ligands and binding sites

CL · Chloride ion · ion · chains H
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains L, H

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

Pockets

5 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	380	0.56	0.75	44	empty
2	176	0.48	0.76	34	empty
3	115	0.37	0.73	26	MES
4	77	0.36	0.76	15	empty
5	87	0.34	0.73	14	empty

Interfaces

1 interface between chains.

L–H · 1709 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5I1C · Crystal structure of human germline antibody IGHV3-23/IGKV3-20 · 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 5I1C · PDBe 5I1C

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