MolNFT v1 · #111340 · protein

Crystal structure of monoclonal anti-human podoplanin antibody nz-1 with bound pa peptide

4YO0 · Heavy chain of antigen binding fragment, Fab: “Crystal structure of monoclonal anti-human podoplanin antibody nz-1 with bound pa peptide”. X-ray diffraction, 8 pockets (best druggability 0.68). MolNFT v1 #111340 on GenesisL1: 3D…

PDB: 4YO0
Type: protein
Length: 850 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heavy chain of antigen binding fragment, Fab; Light chain of antigen binding fragment…
Pockets: 8 · best druggability 0.68

Structure

x-ray diffraction · 5 distinct chains · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heavy chain of antigen binding fragment, Fab	protein	209	6% helix, 55% strand	—
B, D	Light chain of antigen binding fragment, Fab	protein	210	10% helix, 53% strand	—
C	Heavy chain of antigen binding fragment, Fab	protein	198	8% helix, 55% strand	—
E	PA14 peptide	protein	12	0% helix, 0% strand	—
F	PA14 peptide	protein	11	0% helix, 0% strand	—

Ligands and binding sites

EDO · 1,2-ethanediol · additive · chains C, D

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

Pockets

8 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	1140	0.68	0.73	96	empty
2	565	0.61	0.74	57	empty
3	57	0.44	0.83	16	empty
4	66	0.43	0.81	17	empty
5	82	0.33	0.75	19	empty

Interfaces

8 interfaces between chains.

C–D · 1626 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1602 Å² buried · 12 hydrogen bonds · protein-protein
A–E · 627 Å² buried · 12 hydrogen bonds · protein-protein
C–F · 595 Å² buried · 13 hydrogen bonds · protein-protein
B–E · 256 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 modified (disulfide, cyclization).

Compared structures

4YO0 · Crystal structure of monoclonal anti-human podoplanin antibody NZ-1 with bound PA peptide · 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 4YO0 · PDBe 4YO0

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