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Crystal structure of the TEPC15-VK45.1 anti-2-phenyl-5- oxazolone NQ10-1.12 scfv in complex with the hapten

Analyse Crystal structure of the TEPC15-VK45.1 anti-2-phenyl-5- oxazolone NQ10-1.12… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2UUD
Type: protein
Length: 487 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NQ10-1.12 anti-phox antibody
Ligands: PHX
Pockets: 8 · best druggability 0.71

Structure

x-ray diffraction · 4 distinct chains · 5% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, J	NQ10-1.12 anti-phox antibody	protein	121	10% helix, 50% strand	—
K, L	NQ10-1.12 anti-phox antibody	protein	113	0% helix, 37% strand	—
S	NQ10-1.12 anti-phox antibody	protein	9	0% helix, 0% strand	—
T	NQ10-1.12 anti-phox antibody	protein	10	0% helix, 0% strand	—

Ligands and binding sites

PHX · 4-{[(Z)-(5-oxo-2-phenyl-1,3-oxazol-4(5H)-ylidene)methyl]amino}butanoic acid · ligand · 2 copies · chains H, K, L, J

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	178	0.71	0.89	37	empty
2	167	0.48	0.76	28	PHX
3	198	0.47	0.75	28	empty
4	149	0.41	0.74	23	empty
5	103	0.39	0.76	20	PHX

Interfaces

10 interfaces between chains.

H–L · 916 Å² buried · 11 hydrogen bonds · protein-protein
J–K · 912 Å² buried · 12 hydrogen bonds · protein-protein
H–K · 258 Å² buried · 6 hydrogen bonds · protein-protein
J–L · 239 Å² buried · 3 hydrogen bonds · protein-protein
H–S · 107 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

2UUD · Crystal structure of the TEPC15-Vk45.1 anti-2-phenyl-5-oxazolone NQ10- 1.12 scFv in… · the same entry in another collection · chain J against J, 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 2UUD · PDBe 2UUD

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