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Crystal structure of the L-cystine solute receptor of neisseria gonorrhoeae in the unliganded open conformation

Analyse Crystal structure of the L-cystine solute receptor of neisseria gonorrhoeae in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ZSF
Type: protein
Length: 1,892 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ABC transporter, periplasmic binding protein, amino acid
UniProt: Q5F9M1
Pockets: 17 · best druggability 0.88

Structure

x-ray diffraction · 5 distinct chains · 38% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, E	ABC transporter, periplasmic binding protein, amino acid	protein	237	38% helix, 24% strand	Q5F9M1
B	ABC transporter, periplasmic binding protein, amino acid	protein	237	38% helix, 24% strand	Q5F9M1
C, G	ABC transporter, periplasmic binding protein, amino acid	protein	235	39% helix, 24% strand	Q5F9M1
F	ABC transporter, periplasmic binding protein, amino acid	protein	238	38% helix, 24% strand	Q5F9M1
H	ABC transporter, periplasmic binding protein, amino acid	protein	236	39% helix, 23% strand	Q5F9M1

Pockets

17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1011	0.88	0.89	129	empty
2	915	0.87	0.89	116	empty
3	853	0.87	0.90	99	empty
4	1129	0.87	0.88	137	empty
5	306	0.69	0.83	45	empty

Interfaces

11 interfaces between chains.

C–D · 1536 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1521 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 1494 Å² buried · 19 hydrogen bonds · protein-protein
G–H · 1413 Å² buried · 20 hydrogen bonds · protein-protein
B–F · 225 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3ZSF · Crystal structure of the L-cystine solute receptor of Neisseria gonorrhoeae in the… · 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 Q5F9M1
Elsewhere: RCSB PDB 3ZSF · PDBe 3ZSF · UniProt Q5F9M1

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