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Crystal structure of the antibody-binding region of protein M (protein M td) in complex with anti-HIV antibody PGT135 Fab

Analyse Crystal structure of the antibody-binding region of protein M (protein M td) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4NZR
Type: protein
Length: 833 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: PGT135 heavy chain; PGT135 light chain; Protein M td
UniProt: P47523
Pockets: 9 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 14% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	PGT135 heavy chain	protein	228	8% helix, 49% strand	—
L	PGT135 light chain	protein	214	6% helix, 50% strand	—
M	Protein M td	protein	391	23% helix, 28% strand	P47523

Ligands and binding sites

GOL · Glycerol · additive · chains M

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

Pockets

9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1050	0.82	0.84	101	empty
2	276	0.60	0.79	49	empty
3	144	0.50	0.79	29	empty
4	151	0.44	0.75	23	empty
5	108	0.43	0.77	17	empty

Interfaces

3 interfaces between chains.

H–L · 1884 Å² buried · 16 hydrogen bonds · protein-protein
L–M · 1754 Å² buried · 32 hydrogen bonds · protein-protein
H–M · 653 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4NZR · Crystal structure of the antibody-binding region of Protein M (Protein M TD) in complex… · the same entry in another collection · chain H against H, TM-score 1.00
P47523 · AlphaFold monomer V2.0 prediction for uncharacterized protein MG281 (P47523) · a predicted model of the same protein · chain M against A, 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 P47523
Elsewhere: RCSB PDB 4NZR · PDBe 4NZR · UniProt P47523

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