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Crystal structure of the N-terminal domain of the secretin gspd from etec determined with the assistance of a nanobody

Analyse Crystal structure of the N-terminal domain of the secretin gspd from etec… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3EZJ
Type: protein
Length: 1,271 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: General secretion pathway protein gspd; Nanobody NBGSPD_7
UniProt: B3IFK0
Ligands: PO4, CL
Pockets: 19 · best druggability 0.81

Structure

x-ray diffraction · 5 distinct chains · 37% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	General secretion pathway protein gspd	protein	198	40% helix, 32% strand	B3IFK0
C	General secretion pathway protein gspd	protein	197	41% helix, 29% strand	B3IFK0
E	General secretion pathway protein gspd	protein	197	45% helix, 30% strand	B3IFK0
G	General secretion pathway protein gspd	protein	199	41% helix, 31% strand	B3IFK0
B, D, F, H	Nanobody NBGSPD_7	protein	120	5% helix, 60% strand	—

Ligands and binding sites

PO4 · Phosphate ion · ion · 8 copies · chains A, C, E, G, B, F, D, H
CL · Chloride ion · ion · 4 copies · chains B, D, F, H

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

Pockets

19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	764	0.81	0.84	77	empty
2	804	0.76	0.81	81	empty
3	749	0.76	0.81	78	empty
4	335	0.73	0.85	45	empty
5	295	0.71	0.85	40	empty

Interfaces

15 interfaces between chains.

A–B · 1038 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 1006 Å² buried · 24 hydrogen bonds · protein-protein
E–F · 1006 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 979 Å² buried · 24 hydrogen bonds · protein-protein
A–E · 809 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3EZJ · Crystal structure of the N-terminal domain of the secretin GspD from ETEC determined with… · the same entry in another collection · chain B against B, 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 B3IFK0
Elsewhere: RCSB PDB 3EZJ · PDBe 3EZJ · UniProt B3IFK0

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