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X-ray crystal structure of a methylmalonate semialdehyde dehydrogenase from pseudomonas sp. aac

Analyse X-ray crystal structure of a methylmalonate semialdehyde dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5TJR
Type: protein
Length: 2,763 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methylmalonate-semialdehyde dehydrogenase
UniProt: A0A081YAY7
Ligands: ADP
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 6 distinct chains · 42% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methylmalonate-semialdehyde dehydrogenase	protein	460	42% helix, 23% strand	A0A081YAY7
B	Methylmalonate-semialdehyde dehydrogenase	protein	465	43% helix, 25% strand	A0A081YAY7
C	Methylmalonate-semialdehyde dehydrogenase	protein	461	42% helix, 23% strand	A0A081YAY7
D	Methylmalonate-semialdehyde dehydrogenase	protein	468	42% helix, 25% strand	A0A081YAY7
E	Methylmalonate-semialdehyde dehydrogenase	protein	455	43% helix, 23% strand	A0A081YAY7
F	Methylmalonate-semialdehyde dehydrogenase	protein	454	43% helix, 25% strand	A0A081YAY7

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, B, D, E, F

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	1048	0.87	0.88	107	empty
2	1077	0.86	0.87	105	empty
3	1156	0.85	0.86	107	empty
4	122	0.79	0.97	27	empty
5	130	0.77	0.96	31	empty

Interfaces

15 interfaces between chains.

A–F · 2171 Å² buried · 40 hydrogen bonds · protein-protein
B–C · 2146 Å² buried · 41 hydrogen bonds · protein-protein
D–E · 2100 Å² buried · 37 hydrogen bonds · protein-protein
E–F · 758 Å² buried · 9 hydrogen bonds · protein-protein
A–E · 739 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

5TJR · X-ray Crystal structure of a methylmalonate semialdehyde dehydrogenase from Pseudomonas… · 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 A0A081YAY7
Elsewhere: RCSB PDB 5TJR · PDBe 5TJR · UniProt A0A081YAY7

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