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Pcrv fragment with bound Fab

Analyse Pcrv fragment with bound Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6CYF
Type: protein
Length: 2,255 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Type III secretion system protein; IGG1 antibody, kappa light chain; IGG1 antibody, heavy…
UniProt: M4Q7H6
Pockets: 20 · best druggability 0.64

Structure

x-ray diffraction · 8 distinct chains · 18% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, I	Type III secretion system protein	protein	127	53% helix, 3% strand	M4Q7H6
C, L, E, T	IGG1 antibody, kappa light chain	protein	214	7% helix, 50% strand	—
D	IGG1 antibody, heavy chain fragment	protein	224	7% helix, 51% strand	—
B	Type III secretion system protein	protein	126	51% helix, 3% strand	M4Q7H6
M	IGG1 antibody, heavy chain fragment	protein	222	7% helix, 52% strand	—
F	IGG1 antibody, heavy chain fragment	protein	223	7% helix, 52% strand	—
Q	Type III secretion system protein	protein	127	51% helix, 3% strand	M4Q7H6
U	IGG1 antibody, heavy chain fragment	protein	223	7% helix, 52% strand	—

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	712	0.64	0.73	76	empty
2	84	0.61	0.89	22	empty
3	111	0.61	0.86	31	empty
4	110	0.60	0.86	30	empty
5	115	0.60	0.85	30	empty

Interfaces

18 interfaces between chains.

C–D · 2063 Å² buried · 18 hydrogen bonds · protein-protein
L–M · 2028 Å² buried · 18 hydrogen bonds · protein-protein
T–U · 2016 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 2001 Å² buried · 14 hydrogen bonds · protein-protein
D–M · 758 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide (disulfide).

Compared structures

6CYF · PcrV fragment with bound Fab · 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 M4Q7H6
Elsewhere: RCSB PDB 6CYF · PDBe 6CYF · UniProt M4Q7H6

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