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Crystal structure of 3D11 Fab in complex with plasmodium berghei circumsporozoite protein papp peptide

Analyse Crystal structure of 3D11 Fab in complex with plasmodium berghei… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6X8Q
Type: protein
Length: 445 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3D11 Fab heavy chain; 3D11 Fab light chain; Papp peptide
Pockets: 3 · best druggability 0.59

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	3D11 Fab heavy chain	protein	213	10% helix, 50% strand	—
L	3D11 Fab light chain	protein	219	5% helix, 52% strand	—
P	Papp peptide	protein	13	0% helix, 0% strand	—

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 7 copies · chains H, L, P

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

Pockets

3 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	512	0.59	0.74	53	empty
2	61	0.55	0.89	18	EDO
3	76	0.30	0.73	19	empty

Interfaces

3 interfaces between chains.

H–L · 1864 Å² buried · 15 hydrogen bonds · protein-protein
H–P · 436 Å² buried · 11 hydrogen bonds · protein-protein
L–P · 380 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6X8Q · Crystal structure of 3D11 Fab in complex with Plasmodium berghei circumsporozoite protein… · 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 6X8Q · PDBe 6X8Q

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