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Structure of unliganded anti-GP120 CD4BS antibody DH522UCA Fab

Analyse Structure of unliganded anti-GP120 CD4BS antibody DH522UCA Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5UKN
Type: protein
Length: 438 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DH522UCA Fab fragment heavy chain; DH522UCA Fab fragment light chain
Ligands: CL
Pockets: 5 · best druggability 0.47

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	DH522UCA Fab fragment heavy chain	protein	227	7% helix, 52% strand	—
L	DH522UCA Fab fragment light chain	protein	211	6% helix, 53% strand	—

Ligands and binding sites

CL · Chloride ion · ion · chains H, L

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

Pockets

5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	266	0.47	0.73	38	empty
2	78	0.42	0.80	19	empty
3	56	0.37	0.80	18	empty
4	90	0.35	0.75	16	empty
5	75	0.35	0.76	23	empty

Interfaces

1 interface between chains.

H–L · 1955 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5UKN · Structure of unliganded anti-gp120 CD4bs antibody DH522UCA Fab · the same entry in another collection · chain H against H, 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 5UKN · PDBe 5UKN

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