MolNFT v1 · #142421 · protein

Complex structure of 4-1BB and utomilumab

6A3W · Utomilumab vh: “Complex structure of 4-1BB and utomilumab”. X-ray diffraction, 1 ligand (NAG), 16 pockets (best druggability 0.79). MolNFT v1 #142421 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6A3W
Type: protein
Length: 1,367 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Utomilumab vh; Utomilumab vl; Tumor necrosis factor receptor superfamily member 9
UniProt: Q07011
Ligands: NAG
Pockets: 16 · best druggability 0.79

Structure

x-ray diffraction · 7 distinct chains · 4% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, G, J	Utomilumab vh	protein	116	8% helix, 49% strand	—
B	Utomilumab vl	protein	106	6% helix, 50% strand	—
C	Tumor necrosis factor receptor superfamily member 9	protein	135	6% helix, 36% strand	Q07011
E, H, K	Utomilumab vl	protein	107	6% helix, 50% strand	—
F	Tumor necrosis factor receptor superfamily member 9	protein	93	4% helix, 33% strand	Q07011
I	Tumor necrosis factor receptor superfamily member 9	protein	128	2% helix, 38% strand	Q07011
L	Tumor necrosis factor receptor superfamily member 9	protein	120	0% helix, 31% strand	Q07011

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains I

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

Pockets

16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	590	0.79	0.85	81	empty
2	497	0.76	0.84	59	empty
3	677	0.75	0.81	81	empty
4	483	0.75	0.83	66	empty
5	53	0.69	0.97	19	empty

Interfaces

22 interfaces between chains.

D–E · 740 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 739 Å² buried · 12 hydrogen bonds · protein-protein
G–H · 736 Å² buried · 11 hydrogen bonds · protein-protein
J–K · 731 Å² buried · 11 hydrogen bonds · protein-protein
G–I · 618 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 46 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

6A3W · Complex structure of 4-1BB and utomilumab · 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
Every structure of UniProt Q07011
Elsewhere: RCSB PDB 6A3W · PDBe 6A3W · UniProt Q07011

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