Research workbench

Context-independent anti-hypusine antibody FABHPU98.61 in complex with hypusine

Analyse Context-independent anti-hypusine antibody FABHPU98.61 in complex with hypusine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5DTF
Type: protein
Length: 843 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab HPU98.61 heavy chain; Fab HPU98.61 light chain; Peptide: gly-5CT-gly-ala
Ligands: 5CT
Pockets: 3 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 6% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, A	Fab HPU98.61 heavy chain	protein	207	6% helix, 52% strand	—
L	Fab HPU98.61 light chain	protein	211	5% helix, 54% strand	—
B	Fab HPU98.61 light chain	protein	214	7% helix, 53% strand	—
P	Peptide: gly-5CT-gly-ala	protein	4	0% helix, 0% strand	—

Ligands and binding sites

5CT · Hypusine · ligand · chains A, B
EDO · 1,2-ethanediol · additive · 2 copies · chains H, L, A, B

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

Pockets

3 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	1136	0.76	0.78	134	empty
2	206	0.55	0.79	40	empty
3	143	0.43	0.75	22	empty

Interfaces

5 interfaces between chains.

A–B · 1919 Å² buried · 23 hydrogen bonds · protein-protein
H–L · 1879 Å² buried · 23 hydrogen bonds · protein-protein
H–A · 377 Å² buried · 5 hydrogen bonds · protein-protein
L–P · 227 Å² buried · 7 hydrogen bonds · protein-protein
H–P · 225 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 1 modified (disulfide, nonstandard).

Compared structures

5DTF · context-independent anti-hypusine antibody FabHpu98.61 in complex with hypusine · 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 5DTF · PDBe 5DTF

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