MolNFT v1 · #161393 · protein

Molecular scaffolds expand the nanobody toolkit for cryo-EM applications: crystal structure of mb-chopq-NB207

6QD6 · Mb-chopq-NB207,OUTER membrane PROTEIN,MB-chopq-NB207,OUTER…: “Molecular scaffolds expand the nanobody toolkit for cryo-EM applications: crystal structure of mb-chopq-NB207”. X-ray diffraction, 1 ligand (CL), 20 pockets (best…

PDB: 6QD6
Type: protein
Length: 4,346 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mb-chopq-NB207,OUTER membrane PROTEIN,MB-chopq-NB207,OUTER membrane PROTEIN,MB-chopq-NB207
UniProt: B5Z8H1
Ligands: CL
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 10 distinct chains · 43% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mb-chopq-NB207,OUTER membrane PROTEIN,MB-chopq-NB207,OUTER membrane PROTEIN,MB-chopq-NB207	protein	448	44% helix, 21% strand	B5Z8H1
B	Mb-chopq-NB207,OUTER membrane PROTEIN,MB-chopq-NB207,OUTER membrane PROTEIN,MB-chopq-NB207	protein	446	42% helix, 23% strand	B5Z8H1
C	Mb-chopq-NB207,OUTER membrane PROTEIN,MB-chopq-NB207,OUTER membrane PROTEIN,MB-chopq-NB207	protein	431	40% helix, 24% strand	B5Z8H1
D	Mb-chopq-NB207,OUTER membrane PROTEIN,MB-chopq-NB207,OUTER membrane PROTEIN,MB-chopq-NB207	protein	446	44% helix, 21% strand	B5Z8H1
E	Mb-chopq-NB207,OUTER membrane PROTEIN,MB-chopq-NB207,OUTER membrane PROTEIN,MB-chopq-NB207	protein	451	41% helix, 22% strand	B5Z8H1
F	Mb-chopq-NB207,OUTER membrane PROTEIN,MB-chopq-NB207,OUTER membrane PROTEIN,MB-chopq-NB207	protein	457	44% helix, 21% strand	B5Z8H1
G	Mb-chopq-NB207,OUTER membrane PROTEIN,MB-chopq-NB207,OUTER membrane PROTEIN,MB-chopq-NB207	protein	469	42% helix, 22% strand	B5Z8H1
H	Mb-chopq-NB207,OUTER membrane PROTEIN,MB-chopq-NB207,OUTER membrane PROTEIN,MB-chopq-NB207	protein	399	46% helix, 21% strand	B5Z8H1
I	Mb-chopq-NB207,OUTER membrane PROTEIN,MB-chopq-NB207,OUTER membrane PROTEIN,MB-chopq-NB207	protein	419	44% helix, 21% strand	B5Z8H1
J	Mb-chopq-NB207,OUTER membrane PROTEIN,MB-chopq-NB207,OUTER membrane PROTEIN,MB-chopq-NB207	protein	380	42% helix, 23% strand	B5Z8H1

Ligands and binding sites

CL · Chloride ion · ion · chains A

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	948	0.80	0.82	112	empty
2	685	0.77	0.83	81	empty
3	735	0.76	0.81	87	empty
4	979	0.76	0.79	111	empty
5	733	0.76	0.81	82	empty

Interfaces

9 interfaces between chains.

A–B · 1393 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 1294 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 1235 Å² buried · 22 hydrogen bonds · protein-protein
E–F · 1070 Å² buried · 23 hydrogen bonds · protein-protein
I–J · 900 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 38 disulfide (disulfide).

Compared structures

6QD6 · Molecular scaffolds expand the nanobody toolkit for cryo-EM applications: crystal… · 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 B5Z8H1
Elsewhere: RCSB PDB 6QD6 · PDBe 6QD6 · UniProt B5Z8H1

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