MolNFT v1 · #71806 · protein

Crystal structure of human lyase R41M in complex with hmg-CoA

3MP5 · Hydroxymethylglutaryl-CoA lyase: “Crystal structure of human lyase R41M in complex with hmg-CoA”. X-ray diffraction, 2 ligands (HMG, MG), 15 pockets (best druggability 0.83). MolNFT v1 #71806 on GenesisL1: 3D structure, binding…

PDB: 3MP5
Type: protein
Length: 1,764 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hydroxymethylglutaryl-CoA lyase
EC: 4.1.3.4
UniProt: P35914
Ligands: HMG, MG
Pockets: 15 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 45% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, E	Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4)	protein	296	46% helix, 16% strand	P35914
C	Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4)	protein	288	46% helix, 16% strand	P35914
D	Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4)	protein	294	46% helix, 16% strand	P35914
F	Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4)	protein	294	43% helix, 16% strand	P35914

Ligands and binding sites

HMG · 3-hydroxy-3-methylglutaryl-coenzyme A · ligand · chains B
MG · Magnesium ion · metal · 2 copies · chains B, C

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

Pockets

15 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	1134	0.83	0.84	96	empty
2	196	0.76	0.91	30	HMG, MG
3	1097	0.75	0.78	95	empty
4	425	0.73	0.83	39	empty
5	364	0.72	0.83	36	empty

Interfaces

6 interfaces between chains.

E–F · 1235 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1159 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 1119 Å² buried · 9 hydrogen bonds · protein-protein
D–E · 708 Å² buried · 5 hydrogen bonds · protein-protein
A–F · 474 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3MP5 · Crystal Structure of Human Lyase R41M in complex with HMG-CoA · the same entry in another collection · chain F against F, TM-score 1.00
P35914 · AlphaFold monomer V2.0 prediction for hydroxymethylglutaryl-CoA lyase, mitochondrial… · a predicted model of the same protein · chain F 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 P35914
Elsewhere: RCSB PDB 3MP5 · PDBe 3MP5 · UniProt P35914

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