MolNFT v1 · #123624 · protein

Crystal structure of clfa in complex with the Fab fragment of tefibazumab

5JQ6 · Clumping factor a: “Crystal structure of clfa in complex with the Fab fragment of tefibazumab”. X-ray diffraction, 6 pockets (best druggability 0.72). MolNFT v1 #123624 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5JQ6
Type: protein
Length: 736 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Clumping factor a; Tefibazumab Fab fragment heavy chain; Tefibazumab Fab fragment light…
UniProt: G0XY13
Pockets: 6 · best druggability 0.72

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Clumping factor a	protein	320	6% helix, 49% strand	G0XY13
H	Tefibazumab Fab fragment heavy chain	protein	204	10% helix, 49% strand	—
L	Tefibazumab Fab fragment light chain	protein	212	6% helix, 49% strand	—

Pockets

6 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	142	0.72	0.91	26	empty
2	401	0.71	0.83	62	empty
3	130	0.38	0.74	28	empty
4	93	0.35	0.75	23	empty
5	64	0.33	0.76	12	empty

Interfaces

3 interfaces between chains.

H–L · 1575 Å² buried · 14 hydrogen bonds · protein-protein
A–H · 594 Å² buried · 8 hydrogen bonds · protein-protein
A–L · 532 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

5JQ6 · Crystal structure of ClfA in complex with the Fab fragment of Tefibazumab · the same entry in another collection · chain A against A, 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 G0XY13
Elsewhere: RCSB PDB 5JQ6 · PDBe 5JQ6 · UniProt G0XY13

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