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6652 Fab (unbound)

Analyse 6652 Fab (unbound) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5IBU
Type: protein
Length: 873 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 6652 light chain; 6652 heavy chain
Pockets: 7 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 8% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	6652 light chain	protein	215	7% helix, 50% strand	—
G	6652 heavy chain	protein	225	8% helix, 52% strand	—
H	6652 heavy chain	protein	219	8% helix, 53% strand	—
L	6652 light chain	protein	214	7% helix, 49% strand	—

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	958	0.74	0.78	96	empty
2	415	0.57	0.74	53	empty
3	314	0.53	0.75	38	empty
4	51	0.30	0.76	13	empty
5	69	0.29	0.73	15	empty

Interfaces

5 interfaces between chains.

B–G · 1865 Å² buried · 7 hydrogen bonds · protein-protein
H–L · 1773 Å² buried · 11 hydrogen bonds · protein-protein
G–L · 250 Å² buried · 5 hydrogen bonds · protein-protein
B–H · 226 Å² buried · 4 hydrogen bonds · protein-protein
G–H · 109 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

5IBU · 6652 Fab (unbound) · the same entry in another collection · chain B against B, 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 5IBU · PDBe 5IBU

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