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Crystal structure of human germline antibody IGHV1-69/IGKV3-11

Analyse Crystal structure of human germline antibody IGHV1-69/IGKV3-11 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5I16
Type: protein
Length: 848 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab light chain; Fab heavy chain
Pockets: 7 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, A	Fab light chain	protein	211	6% helix, 51% strand	—
H	Fab heavy chain	protein	213	8% helix, 53% strand	—
B	Fab heavy chain	protein	213	7% helix, 53% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 3 copies · chains L, H, A, B
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B

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

Pockets

7 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	1027	0.75	0.78	117	empty
2	253	0.66	0.83	31	empty
3	518	0.61	0.75	52	empty
4	51	0.48	0.87	22	GOL
5	97	0.39	0.76	25	empty

Interfaces

6 interfaces between chains.

A–B · 1722 Å² buried · 13 hydrogen bonds · protein-protein
L–H · 1718 Å² buried · 19 hydrogen bonds · protein-protein
L–A · 395 Å² buried · 12 hydrogen bonds · protein-protein
H–B · 356 Å² buried · 2 hydrogen bonds · protein-protein
H–A · 213 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 modified (disulfide, cyclization).

Compared structures

5I16 · Crystal structure of human germline antibody IGHV1-69/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 5I16 · PDBe 5I16

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