MolNFT v1 · #60024 · protein

Nanobody-aided structure determination of the EPSI:EPSJ pseudopilin heterdimer from vibrio vulnificus

3CFI · Type II secretory pathway, pseudopilin epsi: “Nanobody-aided structure determination of the EPSI:EPSJ pseudopilin heterdimer from vibrio vulnificus”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.85). MolNFT v1…

PDB: 3CFI
Type: protein
Length: 1,393 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Type II secretory pathway, pseudopilin epsi; Type II secretory pathway, pseudopilin epsj…
UniProt: Q7MPZ1, Q7MPZ0
Ligands: CL
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 12 distinct chains · 15% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Type II secretory pathway, pseudopilin epsi	protein	76	25% helix, 37% strand	Q7MPZ1
B	Type II secretory pathway, pseudopilin epsj	protein	160	16% helix, 44% strand	Q7MPZ0
C	Nanobody NBEPSIJ_11	protein	115	8% helix, 47% strand	—
D	Type II secretory pathway, pseudopilin epsi	protein	80	25% helix, 34% strand	Q7MPZ1
E	Type II secretory pathway, pseudopilin epsj	protein	158	16% helix, 44% strand	Q7MPZ0
F	Nanobody NBEPSIJ_11	protein	114	5% helix, 46% strand	—
G	Type II secretory pathway, pseudopilin epsi	protein	74	27% helix, 36% strand	Q7MPZ1
H	Type II secretory pathway, pseudopilin epsj	protein	157	17% helix, 44% strand	Q7MPZ0
I	Nanobody NBEPSIJ_11	protein	116	8% helix, 49% strand	—
J	Type II secretory pathway, pseudopilin epsi	protein	81	25% helix, 32% strand	Q7MPZ1
K	Type II secretory pathway, pseudopilin epsj	protein	153	16% helix, 46% strand	Q7MPZ0
L	Nanobody NBEPSIJ_11	protein	109	8% helix, 44% strand	—

Ligands and binding sites

CL · Chloride ion · ion · 4 copies · chains E, H, B, K

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

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1002	0.85	0.86	76	empty
2	842	0.84	0.86	75	empty
3	984	0.77	0.79	76	CL
4	947	0.76	0.79	84	CL
5	386	0.69	0.82	40	empty

Interfaces

18 interfaces between chains.

B–K · 1130 Å² buried · 13 hydrogen bonds · protein-protein
E–H · 1096 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 777 Å² buried · 12 hydrogen bonds · protein-protein
D–E · 766 Å² buried · 7 hydrogen bonds · protein-protein
H–I · 754 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3CFI · Nanobody-aided structure determination of the EPSI:EPSJ pseudopilin heterdimer from… · 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 Q7MPZ1
Every structure of UniProt Q7MPZ0
Elsewhere: RCSB PDB 3CFI · PDBe 3CFI · UniProt Q7MPZ1 · UniProt Q7MPZ0

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