MolNFT v1 · #95719 · protein

Crystal structure of putative methylmalonate-semialdehyde dehydrogenase from sinorhizobium meliloti 1021 complexed with NAD, target 011934

4IYM: “Crystal structure of putative methylmalonate-semialdehyde dehydrogenase from sinorhizobium meliloti 1021…”. X-ray diffraction, 2 ligands (NAD, MG), 20 pockets (best druggability 0.86). MolNFT v1 #95719 on GenesisL1: 3D structure…

PDB: 4IYM
Type: protein
Length: 7,819 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methylmalonate-semialdehyde dehydrogenase
EC: 1.2.1.27
UniProt: Q92RW4
Ligands: NAD, MG
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 5 distinct chains · 40% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, F, G, J, K, N	Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)	protein	488	40% helix, 24% strand	Q92RW4
C	Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)	protein	491	40% helix, 23% strand	Q92RW4
E	Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)	protein	490	41% helix, 23% strand	Q92RW4
H, I, L, M, P	Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)	protein	489	41% helix, 24% strand	Q92RW4
O	Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)	protein	489	40% helix, 24% strand	Q92RW4

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
MG · Magnesium ion · metal · 6 copies · chains A, F, G, I, O

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	1142	0.86	0.87	76	empty
2	1200	0.86	0.87	76	empty
3	1183	0.85	0.86	73	empty
4	1179	0.85	0.86	71	empty
5	141	0.81	0.98	30	empty

Interfaces

34 interfaces between chains.

C–D · 2688 Å² buried · 36 hydrogen bonds · protein-protein
E–F · 2674 Å² buried · 34 hydrogen bonds · protein-protein
I–J · 2673 Å² buried · 35 hydrogen bonds · protein-protein
O–P · 2670 Å² buried · 35 hydrogen bonds · protein-protein
G–H · 2667 Å² buried · 36 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 291 modified (engineered).

Compared structures

4IYM · Crystal structure of putative methylmalonate-semialdehyde dehydrogenase from… · 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 Q92RW4
Elsewhere: RCSB PDB 4IYM · PDBe 4IYM · UniProt Q92RW4

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.