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Crystal structure of methylmalonate-semialdehyde dehydrogenase (dddc) from oceanimonas doudoroffii

Analyse Crystal structure of methylmalonate-semialdehyde dehydrogenase (dddc) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ZZ7
Type: protein
Length: 5,851 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methylmalonate-semialdehyde dehydrogenase
UniProt: G5CZI2
Ligands: NAD
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 5 distinct chains · 40% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methylmalonate-semialdehyde dehydrogenase	protein	489	40% helix, 24% strand	G5CZI2
B, D, E, F, I, L	Methylmalonate-semialdehyde dehydrogenase	protein	488	40% helix, 24% strand	G5CZI2
C, G, K	Methylmalonate-semialdehyde dehydrogenase	protein	487	40% helix, 24% strand	G5CZI2
H	Methylmalonate-semialdehyde dehydrogenase	protein	486	40% helix, 24% strand	G5CZI2
J	Methylmalonate-semialdehyde dehydrogenase	protein	487	40% helix, 24% strand	G5CZI2

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains A, C, D, E, I, L

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	1134	0.86	0.87	54	empty
2	1127	0.86	0.87	55	empty
3	1173	0.85	0.86	55	empty
4	871	0.78	0.81	82	empty
5	694	0.77	0.82	67	empty

Interfaces

23 interfaces between chains.

A–B · 2990 Å² buried · 61 hydrogen bonds · protein-protein
I–L · 2987 Å² buried · 59 hydrogen bonds · protein-protein
G–H · 2973 Å² buried · 57 hydrogen bonds · protein-protein
E–F · 2958 Å² buried · 56 hydrogen bonds · protein-protein
J–K · 2940 Å² buried · 58 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

4ZZ7 · Crystal structure of methylmalonate-semialdehyde dehydrogenase (DddC) from Oceanimonas… · 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 G5CZI2
Elsewhere: RCSB PDB 4ZZ7 · PDBe 4ZZ7 · UniProt G5CZI2

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