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Crystal structure of NMB1025, a member of yjgf protein family, from neisseria meningitidis (hexagonal crystal form)

Analyse Crystal structure of NMB1025, a member of yjgf protein family, from neisseria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3KJJ
Type: protein
Length: 1,407 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NMB1025 protein
UniProt: Q9JZJ4
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 6 distinct chains · 30% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	NMB1025 protein	protein	117	30% helix, 34% strand	Q9JZJ4
B, C, J, K	NMB1025 protein	protein	119	29% helix, 34% strand	Q9JZJ4
D	NMB1025 protein	protein	118	30% helix, 35% strand	Q9JZJ4
E, H	NMB1025 protein	protein	116	30% helix, 34% strand	Q9JZJ4
G, L	NMB1025 protein	protein	115	30% helix, 33% strand	Q9JZJ4
I	NMB1025 protein	protein	117	30% helix, 33% strand	Q9JZJ4

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, C, B

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	123	0.80	0.98	21	empty
2	77	0.76	0.99	21	empty
3	776	0.76	0.81	97	empty
4	83	0.76	0.98	23	empty
5	962	0.76	0.79	97	empty

Interfaces

21 interfaces between chains.

D–F · 1182 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 1176 Å² buried · 26 hydrogen bonds · protein-protein
B–C · 1160 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1151 Å² buried · 21 hydrogen bonds · protein-protein
H–I · 1144 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 48 modified (engineered).

Compared structures

3KJJ · Crystal structure of NMB1025, a member of YjgF protein family, from Neisseria… · 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 Q9JZJ4
Elsewhere: RCSB PDB 3KJJ · PDBe 3KJJ · UniProt Q9JZJ4

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