MolNFT v1 · #78944 · protein

Crystal structure of human mmachc

3SOM · Methylmalonic aciduria and homocystinuria type C protein: “Crystal structure of human mmachc”. X-ray diffraction, 3 ligands (5AD, B12, DHL), 20 pockets (best druggability 0.79). MolNFT v1 #78944 on GenesisL1: 3D structure, binding…

PDB: 3SOM
Type: protein
Length: 3,659 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methylmalonic aciduria and homocystinuria type C protein
UniProt: Q9Y4U1
Ligands: 5AD, B12, DHL
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 9 distinct chains · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, H, J, K	Methylmalonic aciduria and homocystinuria type C protein	protein	227	40% helix, 18% strand	Q9Y4U1
B, F, G, I	Methylmalonic aciduria and homocystinuria type C protein	protein	228	40% helix, 18% strand	Q9Y4U1
C, O	Methylmalonic aciduria and homocystinuria type C protein	protein	228	41% helix, 18% strand	Q9Y4U1
D	Methylmalonic aciduria and homocystinuria type C protein	protein	229	41% helix, 18% strand	Q9Y4U1
E	Methylmalonic aciduria and homocystinuria type C protein	protein	230	41% helix, 18% strand	Q9Y4U1
L	Methylmalonic aciduria and homocystinuria type C protein	protein	231	40% helix, 18% strand	Q9Y4U1
M	Methylmalonic aciduria and homocystinuria type C protein	protein	231	40% helix, 18% strand	Q9Y4U1
N	Methylmalonic aciduria and homocystinuria type C protein	protein	232	42% helix, 18% strand	Q9Y4U1
P	Methylmalonic aciduria and homocystinuria type C protein	protein	230	40% helix, 18% strand	Q9Y4U1

Ligands and binding sites

5AD · 5'-deoxyadenosine · ligand · 18 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
B12 · Cobalamin · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
DHL · 2-amino-ethanethiol · ligand · 14 copies · chains A, C, D, F, G, H, I, J, K, L, M, N, O, P
FLC · Citrate anion · additive · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
EDO · 1,2-ethanediol · additive · 3 copies · chains E, P

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	907	0.79	0.81	65	B12, FLC
2	957	0.79	0.81	74	B12, FLC, 5AD
3	608	0.75	0.82	45	empty
4	918	0.74	0.78	66	5AD, B12, FLC
5	978	0.74	0.77	72	5AD, B12, FLC

Interfaces

31 interfaces between chains.

E–F · 1087 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1062 Å² buried · 9 hydrogen bonds · protein-protein
M–N · 1057 Å² buried · 7 hydrogen bonds · protein-protein
I–J · 1055 Å² buried · 8 hydrogen bonds · protein-protein
K–L · 1002 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 modified, 10 covalent (engineered, covalent ligand).

Compared structures

3SOM · crystal structure of human MMACHC · the same entry in another collection · chain K against K, 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 Q9Y4U1
Elsewhere: RCSB PDB 3SOM · PDBe 3SOM · UniProt Q9Y4U1

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