MolNFT v1 · #174139 · protein

Crystal structure of FAB1, the Fab fragment of the anti-bama monoclonal antibody MAB1

7BM5 · FAB1 light chain: “Crystal structure of FAB1, the Fab fragment of the anti-bama monoclonal antibody MAB1”. X-ray diffraction, 20 pockets (best druggability 0.73). MolNFT v1 #174139 on GenesisL1: 3D structure, binding sites and…

PDB: 7BM5
Type: protein
Length: 2,443 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: FAB1 light chain; FAB1 heavy chain
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 10 distinct chains · 4% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, A, J	FAB1 light chain	protein	212	4% helix, 49% strand	—
H	FAB1 heavy chain	protein	221	4% helix, 51% strand	—
C	FAB1 light chain	protein	203	4% helix, 46% strand	—
E	FAB1 light chain	protein	190	4% helix, 52% strand	—
G	FAB1 light chain	protein	196	4% helix, 47% strand	—
B	FAB1 heavy chain	protein	216	4% helix, 50% strand	—
D	FAB1 heavy chain	protein	208	6% helix, 48% strand	—
F	FAB1 heavy chain	protein	204	6% helix, 50% strand	—
K	FAB1 heavy chain	protein	216	4% helix, 50% strand	—
I	FAB1 heavy chain	protein	153	2% helix, 44% strand	—

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	357	0.73	0.85	31	empty
2	749	0.69	0.76	82	empty
3	599	0.69	0.78	54	empty
4	613	0.68	0.77	65	empty
5	417	0.68	0.80	61	empty

Interfaces

23 interfaces between chains.

L–H · 1944 Å² buried · 17 hydrogen bonds · protein-protein
J–K · 1747 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1747 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 1735 Å² buried · 12 hydrogen bonds · protein-protein
G–I · 1480 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 22 disulfide (disulfide).

Compared structures

7BM5 · Crystal structure of Fab1, the Fab fragment of the anti-BamA monoclonal antibody MAB1 · 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 7BM5 · PDBe 7BM5

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