MolNFT v1 · #116908 · protein

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

5DS8 · Fab HPU98 heavy chain: “Context-independent anti-hypusine antibody FABHPU98 in complex with hypusine”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.71). MolNFT v1 #116908 on GenesisL1: 3D structure, binding…

PDB: 5DS8
Type: protein
Length: 837 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab HPU98 heavy chain; Fab HOU98 light chain; Tetrapeptide gly-hpu-gly-ala
Ligands: SO4
Pockets: 7 · best druggability 0.71

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fab HPU98 heavy chain	protein	207	6% helix, 53% strand	—
B, L	Fab HOU98 light chain	protein	211	6% helix, 54% strand	—
H	Fab HPU98 heavy chain	protein	204	6% helix, 53% strand	—
P	Tetrapeptide gly-hpu-gly-ala	protein	4	0% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 11 copies · chains A, B, L, H, P
EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, H, L

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	264	0.71	0.86	35	SO4, EDO
2	304	0.60	0.79	35	empty
3	367	0.56	0.74	41	empty
4	237	0.53	0.77	30	empty
5	76	0.51	0.85	24	EDO, SO4

Interfaces

7 interfaces between chains.

H–L · 1873 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 1841 Å² buried · 14 hydrogen bonds · protein-protein
A–H · 495 Å² buried · 13 hydrogen bonds · protein-protein
B–H · 392 Å² buried · 8 hydrogen bonds · protein-protein
H–P · 229 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 3 modified (disulfide, cyclization, nonstandard).

Compared structures

5DS8 · Context-independent anti-hypusine antibody FabHpu98 in complex with hypusine · the same entry in another collection · chain A 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
Elsewhere: RCSB PDB 5DS8 · PDBe 5DS8

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