MolNFT v1 · #138382 · protein

Crystal structure of Fab fragment of antibody dx-2507 bound to fcrn- B2M

5WHK · Dx-2507 Fab heavy chain: “Crystal structure of Fab fragment of antibody dx-2507 bound to fcrn- B2M”. X-ray diffraction, 11 pockets (best druggability 0.75). MolNFT v1 #138382 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5WHK
Type: protein
Length: 776 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dx-2507 Fab heavy chain; Dx-2507 Fab light chain; IgG receptor fcrn large subunit P51…
UniProt: S6BAN1, Q6NS95, P55899, P61769
Pockets: 11 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 11% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Dx-2507 Fab heavy chain	protein	211	8% helix, 50% strand	S6BAN1
L	Dx-2507 Fab light chain	protein	212	6% helix, 51% strand	Q6NS95
A	IgG receptor fcrn large subunit P51	protein	254	23% helix, 43% strand	P55899
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 2 copies · chains H, A
NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	81	0.75	0.97	27	empty
2	181	0.71	0.88	23	NHE
3	435	0.61	0.76	36	empty
4	233	0.54	0.78	44	empty
5	135	0.53	0.81	27	empty

Interfaces

5 interfaces between chains.

H–L · 1570 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1474 Å² buried · 14 hydrogen bonds · protein-protein
L–A · 479 Å² buried · 5 hydrogen bonds · protein-protein
H–A · 463 Å² buried · 6 hydrogen bonds · protein-protein
L–B · 135 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

5WHK · Crystal structure of Fab fragment of antibody DX-2507 bound to FcRn-B2M · the same entry in another collection · chain H against H, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
P55899 · AlphaFold monomer V2.0 prediction for IgG receptor fcrn large subunit P51 (P55899) · a predicted model of the same protein · chain A against A, TM-score 0.95

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt S6BAN1
Every structure of UniProt Q6NS95
Every structure of UniProt P55899
Every structure of UniProt P61769
Elsewhere: RCSB PDB 5WHK · PDBe 5WHK · UniProt S6BAN1 · UniProt Q6NS95 · UniProt P55899 · UniProt P61769

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