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Crystal structure of azotobacter vinelandii L-rhamnose 1-dehydrogenase (NAD bound-form)

Analyse Crystal structure of azotobacter vinelandii L-rhamnose 1-dehydrogenase (NAD… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7B81
Type: protein
Length: 512 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Short-chain DEHYDROGENASE/REDUCTASE sdr
UniProt: C1DMX5
Ligands: NAD
Pockets: 5 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Short-chain DEHYDROGENASE/REDUCTASE sdr	protein	256	45% helix, 16% strand	C1DMX5

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B

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

Pockets

5 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	456	0.74	0.83	50	NAD
2	418	0.68	0.80	59	NAD
3	116	0.45	0.77	25	empty
4	72	0.35	0.77	19	empty
5	60	0.33	0.77	20	empty

Interfaces

1 interface between chains.

A–B · 1572 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

7B81 · Crystal structure of Azotobacter vinelandii L-rhamnose 1-dehydrogenase (NAD bound-form) · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt C1DMX5
Elsewhere: RCSB PDB 7B81 · PDBe 7B81 · UniProt C1DMX5

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