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Crystal structure of nbla from pcc 7120

Analyse Crystal structure of nbla from pcc 7120 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1OJH
Type: protein
Length: 619 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nbla
UniProt: Q8YNP7
Pockets: 4 · best druggability 0.66

Structure

x-ray diffraction · 8 distinct chains · 79% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nbla	protein	52	81% helix, 0% strand	Q8YNP7
B, E, F, H, L	Nbla	protein	50	82% helix, 0% strand	Q8YNP7
C	Nbla	protein	53	77% helix, 0% strand	Q8YNP7
D	Nbla	protein	56	71% helix, 0% strand	Q8YNP7
G	Nbla	protein	53	79% helix, 0% strand	Q8YNP7
I	Nbla	protein	54	76% helix, 0% strand	Q8YNP7
J	Nbla	protein	51	78% helix, 0% strand	Q8YNP7
K	Nbla	protein	50	88% helix, 0% strand	Q8YNP7

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 2 copies · chains A, G, K, L

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	568	0.66	0.77	56	empty
2	436	0.62	0.77	44	empty
3	87	0.32	0.73	17	empty
4	90	0.30	0.72	21	empty

Interfaces

20 interfaces between chains.

C–D · 1685 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1684 Å² buried · 11 hydrogen bonds · protein-protein
I–J · 1671 Å² buried · 13 hydrogen bonds · protein-protein
G–H · 1664 Å² buried · 10 hydrogen bonds · protein-protein
K–L · 1547 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 modified (engineered).

Compared structures

1OJH · Crystal structure of NblA from PCC 7120 · 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 Q8YNP7
Elsewhere: RCSB PDB 1OJH · PDBe 1OJH · UniProt Q8YNP7

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