Research workbench

Anti-HIV-1 Fab 2G12 + MAN5 re-refinement

Analyse Anti-HIV-1 Fab 2G12 + MAN5 re-refinement in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MUB
Type: protein
Length: 869 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: 13 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 7% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab 2G12, light chain	protein	212	6% helix, 53% strand	P0DOX7
H	Fab 2G12, heavy chain	protein	225	7% helix, 52% strand	P0DOX5
K	Fab 2G12, light chain	protein	213	6% helix, 52% strand	P0DOX7
M	Fab 2G12, heavy chain	protein	219	7% helix, 51% strand	P0DOX5

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 8 copies · chains H, L, M, K
BMA · beta-D-mannopyranose · sugar · 2 copies · chains L, H, K, M

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

Pockets

13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	531	0.73	0.81	52	empty
2	435	0.65	0.78	53	empty
3	274	0.63	0.81	46	empty
4	164	0.50	0.78	31	empty
5	99	0.42	0.78	22	empty

Interfaces

6 interfaces between chains.

H–K · 1126 Å² buried · 11 hydrogen bonds · protein-protein
L–H · 997 Å² buried · 14 hydrogen bonds · protein-protein
H–M · 989 Å² buried · 13 hydrogen bonds · protein-protein
K–M · 976 Å² buried · 11 hydrogen bonds · protein-protein
L–M · 912 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6MUB · Anti-HIV-1 Fab 2G12 + Man5 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 6MUB · PDBe 6MUB · UniProt P0DOX7 · UniProt P0DOX5

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