Research workbench

Crystal structure of S-2-hydroxypropyl coenzyme M dehydrogenase (S- hpcdh) bound to S-hpc and NADH

Analyse Crystal structure of S-2-hydroxypropyl coenzyme M dehydrogenase (S- hpcdh)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ITU
Type: protein
Length: 998 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Short-chain DEHYDROGENASE/REDUCTASE sdr
UniProt: A7IQH5
Ligands: NAI, 1HS
Pockets: 9 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 50% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Short-chain DEHYDROGENASE/REDUCTASE sdr	protein	253	50% helix, 17% strand	A7IQH5
B	Short-chain DEHYDROGENASE/REDUCTASE sdr	protein	250	50% helix, 17% strand	A7IQH5
C	Short-chain DEHYDROGENASE/REDUCTASE sdr	protein	246	50% helix, 17% strand	A7IQH5
D	Short-chain DEHYDROGENASE/REDUCTASE sdr	protein	249	51% helix, 17% strand	A7IQH5

Ligands and binding sites

NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
1HS · 2-{[(2S)-2-hydroxypropyl]sulfanyl}ethanesulfonic acid · ligand · 4 copies · chains A, B, C, D

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

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	914	0.85	0.87	67	empty
2	1166	0.82	0.83	115	NAI, 1HS
3	1146	0.82	0.83	119	NAI, 1HS
4	82	0.42	0.79	14	empty
5	60	0.37	0.79	12	empty

Interfaces

6 interfaces between chains.

C–D · 1419 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 1417 Å² buried · 29 hydrogen bonds · protein-protein
B–D · 1374 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 1364 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 219 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4ITU · Crystal structure of S-2-HYDROXYPROPYL COENZYME M DEHYDROGENASE (S-HPCDH) bound to S-HPC… · 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 A7IQH5
Elsewhere: RCSB PDB 4ITU · PDBe 4ITU · UniProt A7IQH5

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.