MolNFT v1 · #15669 · protein

Glycerol dehydratase reactivase

1NBW · Glycerol dehydratase reactivase alpha subunit: “Glycerol dehydratase reactivase”. X-ray diffraction, 1 ligand (CA), 12 pockets (best druggability 0.83). MolNFT v1 #15669 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1NBW
Type: protein
Length: 1,436 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycerol dehydratase reactivase alpha subunit; Glycerol dehydratase reactivase beta…
UniProt: Q59474, Q48423
Ligands: CA
Pockets: 12 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 33% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycerol dehydratase reactivase alpha subunit	protein	606	33% helix, 31% strand	Q59474
B, D	Glycerol dehydratase reactivase beta subunit	protein	113	35% helix, 22% strand	Q48423
C	Glycerol dehydratase reactivase alpha subunit	protein	604	33% helix, 30% strand	Q59474

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains C, D, A, B

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

Pockets

12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1052	0.83	0.84	115	empty
2	944	0.77	0.80	103	empty
3	762	0.77	0.81	118	empty
4	331	0.64	0.80	41	empty
5	280	0.53	0.75	29	empty

Interfaces

6 interfaces between chains.

A–C · 2117 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 804 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 799 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 388 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 384 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

1NBW · Glycerol dehydratase reactivase · 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 Q59474
Every structure of UniProt Q48423
Elsewhere: RCSB PDB 1NBW · PDBe 1NBW · UniProt Q59474 · UniProt Q48423

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