MolNFT v1 · #137171 · protein

Alternative model for Fab 36-65

5VGA · Fab 36-65 light chain: “Alternative model for Fab 36-65”. X-ray diffraction, 6 pockets (best druggability 0.56). MolNFT v1 #137171 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5VGA
Type: protein
Length: 438 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab 36-65 light chain; Fab 36-65 heavy chain
Pockets: 6 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fab 36-65 light chain	protein	214	7% helix, 50% strand	—
B	Fab 36-65 heavy chain	protein	224	5% helix, 52% strand	—

Ligands and binding sites

PGE · Triethylene glycol · additive · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	417	0.56	0.74	58	empty
2	136	0.47	0.78	20	PGE
3	109	0.40	0.76	21	empty
4	113	0.39	0.75	24	empty
5	52	0.32	0.77	16	empty

Interfaces

1 interface between chains.

A–B · 2006 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5VGA · Alternative model for Fab 36-65 · 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 5VGA · PDBe 5VGA

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