MolNFT v1 · #167349 · protein

Structure of the unaligned FAB4

6VI2 · FAB4 light chain: “Structure of the unaligned FAB4”. X-ray diffraction, 10 pockets (best druggability 0.74). MolNFT v1 #167349 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6VI2
Type: protein
Length: 897 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: FAB4 light chain; FAB4 heavy chain
Pockets: 10 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	FAB4 light chain	protein	215	6% helix, 51% strand	—
B	FAB4 heavy chain	protein	231	5% helix, 52% strand	—
D	FAB4 heavy chain	protein	236	6% helix, 50% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	890	0.74	0.78	104	empty
2	497	0.59	0.74	66	empty
3	56	0.58	0.91	18	empty
4	345	0.57	0.76	38	empty
5	288	0.56	0.77	38	empty

Interfaces

5 interfaces between chains.

A–B · 2045 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 2017 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 607 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 132 Å² buried · 1 hydrogen bond · protein-protein
A–C · 54 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6VI2 · Structure of the unaligned Fab4 · 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 6VI2 · PDBe 6VI2

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