MolNFT v1 · #121631 · protein

Crystal structure of human germline antibody IGHV1-69/IGKV1-39

5I15 · Fab light chain: “Crystal structure of human germline antibody IGHV1-69/IGKV1-39”. X-ray diffraction, 4 pockets (best druggability 0.64). MolNFT v1 #121631 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5I15
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 0.64

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab light chain	protein	214	6% helix, 51% strand	—
H	Fab heavy chain	protein	213	7% helix, 53% strand	—

Ligands and binding sites

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

4 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	654	0.64	0.74	58	empty
2	141	0.42	0.74	28	empty
3	99	0.36	0.74	22	empty
4	61	0.33	0.77	14	MES

Interfaces

1 interface between chains.

L–H · 1698 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5I15 · Crystal structure of human germline antibody IGHV1-69/IGKV1-39 · 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 5I15 · PDBe 5I15

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