MolNFT v1 · #26011 · protein

Plp-dependent catalytic antibody 15A9 in complex with its hapten

1WCB · Fab fragment of catalytic antibody 15A9, light chain: “Plp-dependent catalytic antibody 15A9 in complex with its hapten”. X-ray diffraction, 2 ligands (PE1, IOD), 9 pockets (best druggability 0.76). MolNFT v1 #26011 on GenesisL1: 3D…

PDB: 1WCB
Type: protein
Length: 872 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab fragment of catalytic antibody 15A9, light chain; Fab fragment of catalytic antibody…
Ligands: PE1, IOD
Pockets: 9 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, L	Fab fragment of catalytic antibody 15A9, light chain	protein	213	5% helix, 51% strand	—
B	Fab fragment of catalytic antibody 15A9, heavy chain	protein	224	8% helix, 49% strand	—
H	Fab fragment of catalytic antibody 15A9, heavy chain	protein	222	8% helix, 47% strand	—

Ligands and binding sites

PE1 · N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-lysine · ligand · 2 copies · chains A, B, H, L
IOD · Iodide ion · ion · 9 copies · chains B, H, L

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

Pockets

9 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	1016	0.76	0.78	106	IOD
2	479	0.60	0.75	62	empty
3	309	0.56	0.76	42	empty
4	223	0.53	0.77	28	empty
5	244	0.52	0.76	44	empty

Interfaces

6 interfaces between chains.

A–B · 1747 Å² buried · 11 hydrogen bonds · protein-protein
H–L · 1684 Å² buried · 9 hydrogen bonds · protein-protein
B–L · 304 Å² buried · 2 hydrogen bonds · protein-protein
B–H · 108 Å² buried · 3 hydrogen bonds · protein-protein
A–H · 70 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

1WCB · Plp-dependent catalytic antibody 15A9 in complex with its hapten · 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 1WCB · PDBe 1WCB

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