MolNFT v1 · #183064 · protein

Crystal structure of tphc in an open conformation

7NDR · Tripartite tricarboxylate transporter substrate binding…: “Crystal structure of tphc in an open conformation”. X-ray diffraction, 20 pockets (best druggability 0.66). MolNFT v1 #183064 on GenesisL1: 3D structure, binding sites and…

PDB: 7NDR
Type: protein
Length: 1,757 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tripartite tricarboxylate transporter substrate binding protein
UniProt: A0A5N7XFM8
Pockets: 20 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tripartite tricarboxylate transporter substrate binding protein	protein	294	44% helix, 20% strand	A0A5N7XFM8
B, D, F	Tripartite tricarboxylate transporter substrate binding protein	protein	293	44% helix, 20% strand	A0A5N7XFM8
C, E	Tripartite tricarboxylate transporter substrate binding protein	protein	292	44% helix, 20% strand	A0A5N7XFM8

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 2 copies · chains C, D, E

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	438	0.66	0.79	65	EDO
2	408	0.66	0.79	48	empty
3	437	0.65	0.78	44	empty
4	434	0.65	0.78	58	empty
5	393	0.63	0.78	42	empty

Interfaces

9 interfaces between chains.

E–F · 773 Å² buried · 15 hydrogen bonds · protein-protein
B–F · 759 Å² buried · 14 hydrogen bonds · protein-protein
B–E · 755 Å² buried · 12 hydrogen bonds · protein-protein
D–E · 532 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 482 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

7NDR · Crystal structure of TphC in an open conformation · 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 A0A5N7XFM8
Elsewhere: RCSB PDB 7NDR · PDBe 7NDR · UniProt A0A5N7XFM8

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