MolNFT v1 · #61922 · protein

Crystal structure of a putative dehydrogenase from xanthomonas campestris

3E03 · Short chain dehydrogenase: “Crystal structure of a putative dehydrogenase from xanthomonas campestris”. X-ray diffraction, 1 ligand (CA), 7 pockets (best druggability 0.78). MolNFT v1 #61922 on GenesisL1: 3D structure, binding sites…

PDB: 3E03
Type: protein
Length: 810 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Short chain dehydrogenase
UniProt: Q8P5Q1
Ligands: CA
Pockets: 7 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 46% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Short chain dehydrogenase	protein	267	45% helix, 15% strand	Q8P5Q1
B	Short chain dehydrogenase	protein	271	46% helix, 15% strand	Q8P5Q1
C	Short chain dehydrogenase	protein	272	46% helix, 14% strand	Q8P5Q1

Ligands and binding sites

CA · Calcium ion · metal · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	390	0.78	0.87	43	empty
2	1139	0.78	0.80	117	empty
3	495	0.76	0.84	44	empty
4	465	0.67	0.79	42	empty
5	105	0.45	0.78	22	empty

Interfaces

3 interfaces between chains.

A–B · 408 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 336 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 229 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 17 modified (engineered).

Compared structures

3E03 · Crystal structure of a putative dehydrogenase from Xanthomonas campestris · the same entry in another collection · chain B against B, 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 Q8P5Q1
Elsewhere: RCSB PDB 3E03 · PDBe 3E03 · UniProt Q8P5Q1

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