MolNFT v1 · #34955 · protein

Crystal structure of D-tartrate dehydratase from bradyrhizobium japonicum complexed with mg++ and meso- tartrate

2DW7 · BLL6730 protein: “Crystal structure of D-tartrate dehydratase from bradyrhizobium japonicum complexed with mg++ and meso…”. X-ray diffraction, 2 ligands (SRT, MG), 20 pockets (best druggability 0.85). MolNFT v1 #34955 on GenesisL1…

PDB: 2DW7
Type: protein
Length: 6,208 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BLL6730 protein
EC: 4.2.1.81
UniProt: Q89FH0
Ligands: SRT, MG
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	BLL6730 protein (EC 4.2.1.81)	protein	388	38% helix, 19% strand	Q89FH0

Ligands and binding sites

SRT · S,R meso-tartaric acid · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
MG · Magnesium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, 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, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	922	0.85	0.87	108	empty
2	1041	0.85	0.86	122	empty
3	1011	0.84	0.85	98	empty
4	1128	0.84	0.85	112	empty
5	1054	0.79	0.81	82	empty

Interfaces

34 interfaces between chains.

O–P · 1904 Å² buried · 29 hydrogen bonds · protein-protein
M–N · 1889 Å² buried · 31 hydrogen bonds · protein-protein
K–L · 1889 Å² buried · 31 hydrogen bonds · protein-protein
C–D · 1884 Å² buried · 36 hydrogen bonds · protein-protein
E–F · 1879 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

2DW7 · Crystal structure of D-tartrate dehydratase from Bradyrhizobium japonicum complexed with… · the same entry in another collection · chain P against P, 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 Q89FH0
Elsewhere: RCSB PDB 2DW7 · PDBe 2DW7 · UniProt Q89FH0

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