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Crystal structure of human anti-HIV-1 GP120-reactive antibody E51

Analyse Crystal structure of human anti-HIV-1 GP120-reactive antibody E51 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1RZF
Type: protein
Length: 431 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab E51 light chain; Fab E51 heavy chain
Pockets: 4 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab E51 light chain	protein	213	9% helix, 50% strand	—
H	Fab E51 heavy chain	protein	218	9% helix, 51% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 13 copies · chains L, H
IPA · Isopropyl alcohol · additive · 2 copies · chains L, H

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

Pockets

4 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	447	0.58	0.74	51	GOL, IPA
2	203	0.53	0.77	25	GOL
3	56	0.48	0.85	20	GOL
4	118	0.40	0.75	26	GOL

Interfaces

1 interface between chains.

L–H · 1572 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1RZF · Crystal structure of Human anti-HIV-1 GP120-reactive antibody E51 · 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 1RZF · PDBe 1RZF

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