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Structure of malonyl-coenzyme a reductase from crenarchaeota

Analyse Structure of malonyl-coenzyme a reductase from crenarchaeota in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4DPK
Type: protein
Length: 1,416 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Malonyl-COA/SUCCINYL-CoA reductase
EC: 1.2.1.75, 1.2.1.76
UniProt: Q96YK1
Ligands: PO4
Pockets: 17 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Malonyl-COA/SUCCINYL-CoA reductase (EC 1.2.1.75, 1.2.1.76)	protein	354	33% helix, 23% strand	Q96YK1

Ligands and binding sites

PO4 · Phosphate ion · ion · 12 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	162	0.82	0.98	30	empty
2	129	0.74	0.93	25	empty
3	609	0.70	0.78	75	empty
4	555	0.66	0.77	64	PO4
5	357	0.62	0.78	46	PO4

Interfaces

6 interfaces between chains.

A–B · 1754 Å² buried · 37 hydrogen bonds · protein-protein
C–D · 1753 Å² buried · 39 hydrogen bonds · protein-protein
B–C · 767 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 764 Å² buried · 15 hydrogen bonds · protein-protein
B–D · 649 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4DPK · Structure of malonyl-coenzyme A reductase from crenarchaeota · the same entry in another collection · chain A against A, TM-score 1.00
Q96YK1 · AlphaFold monomer V2.0 prediction for malonyl-CoA reductase (Q96YK1) · a predicted model of the same protein · 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 Q96YK1
Elsewhere: RCSB PDB 4DPK · PDBe 4DPK · UniProt Q96YK1

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