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Crystal structure of HIV-1 neutralizing antibody M66 in complex with GP41 mper peptide

Analyse Crystal structure of HIV-1 neutralizing antibody M66 in complex with GP41 mper… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4NRX
Type: protein
Length: 1,346 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Envelope glycoprotein GP41; M66 heavy chain; M66 light chain
UniProt: Q9QQN5
Pockets: 14 · best druggability 0.73

Structure

x-ray diffraction · 8 distinct chains · 8% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P	Envelope glycoprotein GP41	protein	14	36% helix, 0% strand	Q9QQN5
C	Envelope glycoprotein GP41	protein	13	38% helix, 0% strand	Q9QQN5
H	M66 heavy chain	protein	231	8% helix, 53% strand	—
A	M66 heavy chain	protein	229	8% helix, 52% strand	—
D	M66 heavy chain	protein	228	9% helix, 53% strand	—
L	M66 light chain	protein	213	6% helix, 50% strand	—
B	M66 light chain	protein	207	6% helix, 51% strand	—
E	M66 light chain	protein	211	6% helix, 50% strand	—

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	642	0.73	0.80	64	empty
2	741	0.70	0.77	96	empty
3	902	0.70	0.76	70	empty
4	188	0.56	0.80	35	empty
5	262	0.56	0.77	25	empty

Interfaces

9 interfaces between chains.

D–E · 2052 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1998 Å² buried · 15 hydrogen bonds · protein-protein
H–L · 1970 Å² buried · 14 hydrogen bonds · protein-protein
H–A · 946 Å² buried · 12 hydrogen bonds · protein-protein
L–E · 851 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

4NRX · Crystal Structure of HIV-1 Neutralizing Antibody m66 in complex with gp41 MPER peptide · the same entry in another collection · chain P against P, 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 Q9QQN5
Elsewhere: RCSB PDB 4NRX · PDBe 4NRX · UniProt Q9QQN5

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