MolNFT v1 · #160226 · protein

Crystal structure of CD40 complexed to FAB516

6PE9 · Fab heavy chain: “Crystal structure of CD40 complexed to FAB516”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.78). MolNFT v1 #160226 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6PE9
Type: protein
Length: 2,454 residues
Chains: 15
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab heavy chain; Fab light chain; Tumor necrosis factor receptor superfamily member 5
UniProt: P25942
Ligands: SO4
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 12 distinct chains · 5% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Fab heavy chain	protein	213	8% helix, 52% strand	—
B	Fab light chain	protein	219	5% helix, 52% strand	—
D, F, L	Fab light chain	protein	220	5% helix, 51% strand	—
E	Fab heavy chain	protein	210	4% helix, 55% strand	—
G	Tumor necrosis factor receptor superfamily member 5	protein	121	2% helix, 36% strand	P25942
H	Fab heavy chain	protein	214	9% helix, 54% strand	—
I	Tumor necrosis factor receptor superfamily member 5	protein	97	0% helix, 35% strand	P25942
J	Tumor necrosis factor receptor superfamily member 5	protein	81	4% helix, 32% strand	P25942
K	Fab heavy chain	protein	116	5% helix, 52% strand	—
M	Fab light chain	protein	113	3% helix, 50% strand	—
U	Tumor necrosis factor receptor superfamily member 5	protein	119	3% helix, 32% strand	P25942
V	Tumor necrosis factor receptor superfamily member 5	protein	78	4% helix, 22% strand	P25942

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, H, L, I, U

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1172	0.78	0.80	123	empty
2	246	0.76	0.90	46	empty
3	905	0.74	0.78	93	SO4
4	68	0.70	0.96	27	empty
5	1128	0.69	0.74	110	SO4

Interfaces

26 interfaces between chains.

C–D · 1730 Å² buried · 7 hydrogen bonds · protein-protein
H–L · 1719 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 1712 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1688 Å² buried · 10 hydrogen bonds · protein-protein
I–U · 770 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 49 disulfide (disulfide).

Compared structures

6PE9 · Crystal Structure of CD40 complexed to FAB516 · the same entry in another collection · chain V against V, 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
Every structure of UniProt P25942
Elsewhere: RCSB PDB 6PE9 · PDBe 6PE9 · UniProt P25942

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