MolNFT v1 · #157280 · protein

Anti-HIV-1 Fab 2G12 + MAN7 re-refinement

6MU3 · Fab 2G12, light chain: “Anti-HIV-1 Fab 2G12 + MAN7 re-refinement”. X-ray diffraction, 2 ligands (MAN, BMA), 8 pockets (best druggability 0.69). MolNFT v1 #157280 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6MU3
Type: protein
Length: 856 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab 2G12, light chain; Fab 2G12, heavy chain
UniProt: P0DOX7, P0DOX5
Ligands: MAN, BMA
Pockets: 8 · best druggability 0.69

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, K	Fab 2G12, light chain	protein	211	6% helix, 54% strand	P0DOX7
H	Fab 2G12, heavy chain	protein	218	7% helix, 52% strand	P0DOX5
M	Fab 2G12, heavy chain	protein	216	7% helix, 51% strand	P0DOX5

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 6 copies · chains L, H, K, M
BMA · beta-D-mannopyranose · sugar · 2 copies · chains H, M

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

Pockets

8 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	385	0.69	0.82	37	empty
2	410	0.65	0.78	49	empty
3	267	0.61	0.80	49	empty
4	119	0.47	0.79	27	empty
5	112	0.35	0.73	24	empty

Interfaces

6 interfaces between chains.

H–M · 989 Å² buried · 14 hydrogen bonds · protein-protein
L–H · 983 Å² buried · 9 hydrogen bonds · protein-protein
K–M · 942 Å² buried · 9 hydrogen bonds · protein-protein
H–K · 919 Å² buried · 8 hydrogen bonds · protein-protein
L–M · 909 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6MU3 · Anti-HIV-1 Fab 2G12 + Man7 re-refinement · the same entry in another collection · chain L against L, TM-score 1.00
P0DOX7 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa light chain (P0DOX7) · a predicted model of the same protein · chain L against A, TM-score 0.83

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 P0DOX7
Every structure of UniProt P0DOX5
Elsewhere: RCSB PDB 6MU3 · PDBe 6MU3 · UniProt P0DOX7 · UniProt P0DOX5

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