MolNFT v1 · #64981 · protein

Rational development of high-affinity T-cell receptor-like antibodies

3GJE · Fab light chain: “Rational development of high-affinity T-cell receptor-like antibodies”. X-ray diffraction, 11 pockets (best druggability 0.71). MolNFT v1 #64981 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3GJE
Type: protein
Length: 864 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab light chain; Fab heavy chain
Pockets: 11 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, A	Fab light chain	protein	212	6% helix, 50% strand	—
H, B	Fab heavy chain	protein	220	10% helix, 51% strand	—

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1043	0.71	0.75	102	empty
2	831	0.70	0.76	90	empty
3	787	0.70	0.76	69	empty
4	805	0.68	0.75	78	empty
5	84	0.47	0.82	19	empty

Interfaces

6 interfaces between chains.

A–B · 1743 Å² buried · 11 hydrogen bonds · protein-protein
L–H · 1702 Å² buried · 12 hydrogen bonds · protein-protein
H–B · 1037 Å² buried · 7 hydrogen bonds · protein-protein
L–A · 250 Å² buried · 1 hydrogen bond · protein-protein
H–A · 115 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

3GJE · Rational development of high-affinity T-cell receptor-like antibodies · 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 3GJE · PDBe 3GJE

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