MolNFT v1 · #116849 · protein

Structure of unliganded S55-5 Fab

5DQJ · S55-5 Fab (IGG1 kappa) light chain: “Structure of unliganded S55-5 Fab”. X-ray diffraction, 12 pockets (best druggability 0.77). MolNFT v1 #116849 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DQJ
Type: protein
Length: 878 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: S55-5 Fab (IGG1 kappa) light chain; S55-5 Fab (IGG1) heavy chain
Pockets: 12 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, B	S55-5 Fab (IGG1 kappa) light chain	protein	217	6% helix, 53% strand	—
H, A	S55-5 Fab (IGG1) heavy chain	protein	222	7% helix, 50% strand	—

Pockets

12 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	550	0.77	0.84	85	empty
2	256	0.56	0.78	41	empty
3	219	0.52	0.77	32	empty
4	59	0.43	0.82	15	empty
5	128	0.43	0.76	17	empty

Interfaces

6 interfaces between chains.

L–H · 2101 Å² buried · 18 hydrogen bonds · protein-protein
B–A · 2033 Å² buried · 24 hydrogen bonds · protein-protein
L–A · 367 Å² buried · 2 hydrogen bonds · protein-protein
H–B · 54 Å² buried · 0 hydrogen bonds · protein-protein
H–A · 33 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5DQJ · Structure of unliganded S55-5 Fab · the same entry in another collection · chain H against H, 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 5DQJ · PDBe 5DQJ

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