MolNFT v1 · #172212 · protein

TERBIUM(III)-bound de novo tim barrel-ferredoxin fold fusion dimer with 4-glutamate binding site and tryptophan antenna (tfd-ee N6W)

6ZV9: “TERBIUM(III)-bound de novo tim barrel-ferredoxin fold fusion dimer with 4-glutamate binding site and…”. X-ray diffraction, 1 ligand (TB), 4 pockets (best druggability 0.78). MolNFT v1 #172212 on GenesisL1: 3D structure, binding…

PDB: 6ZV9
Type: protein
Length: 335 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tfd-ee
Ligands: TB
Pockets: 4 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tfd-ee	protein	166	46% helix, 27% strand	—
B	Tfd-ee	protein	169	47% helix, 27% strand	—

Ligands and binding sites

TB · Terbium(iii) ion · metal · chains A, B
EDO · 1,2-ethanediol · additive · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	537	0.78	0.85	69	EDO
2	70	0.52	0.85	21	empty
3	113	0.45	0.79	20	empty
4	81	0.37	0.76	18	empty

Interfaces

1 interface between chains.

A–B · 2042 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

6ZV9 · Terbium(III)-bound de novo TIM barrel-ferredoxin fold fusion dimer with 4-glutamate… · 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
Elsewhere: RCSB PDB 6ZV9 · PDBe 6ZV9

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