MolNFT v1 · #123812 · protein

Structure of MEDI8852 Fab fragment

5JW5 · MEDI8852 heavy chain: “Structure of MEDI8852 Fab fragment”. X-ray diffraction, 1 ligand (PO4), 13 pockets (best druggability 0.76). MolNFT v1 #123812 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5JW5
Type: protein
Length: 862 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MEDI8852 heavy chain; MEDI8852 light chain
Ligands: PO4
Pockets: 13 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 6% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	MEDI8852 heavy chain	protein	224	6% helix, 52% strand	—
L	MEDI8852 light chain	protein	209	6% helix, 53% strand	—
A	MEDI8852 heavy chain	protein	223	6% helix, 52% strand	—
B	MEDI8852 light chain	protein	206	6% helix, 53% strand	—

Ligands and binding sites

PO4 · Phosphate ion · ion · 3 copies · chains H, L, A, B

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

Pockets

13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	514	0.76	0.83	55	empty
2	760	0.71	0.77	50	empty
3	68	0.46	0.83	16	empty
4	66	0.45	0.82	19	empty
5	97	0.44	0.79	18	PO4

Interfaces

6 interfaces between chains.

A–B · 1684 Å² buried · 15 hydrogen bonds · protein-protein
H–L · 1683 Å² buried · 16 hydrogen bonds · protein-protein
H–A · 577 Å² buried · 3 hydrogen bonds · protein-protein
L–B · 313 Å² buried · 6 hydrogen bonds · protein-protein
H–B · 90 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5JW5 · Structure of MEDI8852 Fab Fragment · 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 5JW5 · PDBe 5JW5

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