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Anti HIV1 protease Fab complex

Analyse Anti HIV1 protease Fab complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1MF2
Type: protein
Length: 872 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Monoclonal antibody F11.2.32
Pockets: 9 · best druggability 0.77

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, M	Monoclonal antibody F11.2.32	protein	215	4% helix, 51% strand	—
H, N	Monoclonal antibody F11.2.32	protein	221	9% helix, 54% strand	—

Pockets

9 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	1119	0.77	0.79	112	empty
2	1095	0.75	0.78	101	empty
3	139	0.56	0.83	21	empty
4	144	0.47	0.78	29	empty
5	73	0.32	0.74	21	empty

Interfaces

6 interfaces between chains.

M–N · 1869 Å² buried · 14 hydrogen bonds · protein-protein
L–H · 1860 Å² buried · 15 hydrogen bonds · protein-protein
H–N · 859 Å² buried · 7 hydrogen bonds · protein-protein
L–M · 431 Å² buried · 6 hydrogen bonds · protein-protein
L–N · 76 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

1MF2 · Anti HIV1 protease Fab complex · 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 1MF2 · PDBe 1MF2

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