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Structure of 2G12 IgG dimer

Analyse Structure of 2G12 IgG dimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4NHH
Type: protein
Length: 3,750 residues
Chains: 18
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2G12 IgG dimer light chain; Hepatitis B virus receptor binding protein; 2G12 IgG dimer…
UniProt: Q6PYX1
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 8 distinct chains · 6% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, K, G, F, Q, P	2G12 IgG dimer light chain	protein	211	5% helix, 53% strand	—
H	Hepatitis B virus receptor binding protein	protein	209	6% helix, 47% strand	Q6PYX1
M, R	Hepatitis B virus receptor binding protein	protein	206	4% helix, 48% strand	Q6PYX1
A, C, J	2G12 IgG dimer heavy chain	protein	207	5% helix, 44% strand	—
B, D, N	2G12 IgG dimer heavy chain	protein	206	10% helix, 38% strand	—
E	Hepatitis B virus receptor binding protein	protein	210	6% helix, 47% strand	Q6PYX1
I	Hepatitis B virus receptor binding protein	protein	206	4% helix, 48% strand	Q6PYX1
O	Hepatitis B virus receptor binding protein	protein	208	6% helix, 48% strand	Q6PYX1

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	937	0.76	0.79	117	empty
2	863	0.74	0.79	100	empty
3	989	0.73	0.77	84	empty
4	644	0.71	0.79	61	empty
5	366	0.68	0.81	44	empty

Interfaces

40 interfaces between chains.

A–B · 1179 Å² buried · 8 hydrogen bonds · protein-protein
J–N · 1178 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 1176 Å² buried · 8 hydrogen bonds · protein-protein
L–M · 965 Å² buried · 9 hydrogen bonds · protein-protein
G–I · 962 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 36 disulfide (disulfide).

Compared structures

4NHH · Structure of 2G12 IgG Dimer · 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
Every structure of UniProt Q6PYX1
Elsewhere: RCSB PDB 4NHH · PDBe 4NHH · UniProt Q6PYX1

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