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Crystal structure of the T. vaginalis initiator binding protein bound to the ferredoxin inr

Analyse Crystal structure of the T. vaginalis initiator binding protein bound to the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1PP7
Type: protein + DNA
Length: 139 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ferredoxin inr; 39 kda initiator binding protein
UniProt: Q95VR4
Ligands: ZN
Pockets: 2 · best druggability 0.38

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Ferredoxin inr	dna	12	—	—
F	Ferredoxin inr	dna	13	—	—
U	39 kda initiator binding protein	protein	114	47% helix, 19% strand	Q95VR4

Ligands and binding sites

ZN · Zinc ion · metal · 7 copies · chains E, F, U

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	89	0.38	0.77	23	empty
2	71	0.33	0.75	17	empty

Interfaces

3 interfaces between chains.

E–U · 559 Å² buried · 12 hydrogen bonds · protein-nucleic
F–U · 541 Å² buried · 7 hydrogen bonds · protein-nucleic
E–F · 533 Å² buried · 48 hydrogen bonds · nucleic-nucleic

Compared structures

1PP7 · Crystal structure of the T. vaginalis Initiator binding protein bound to the ferredoxin… · the same entry in another collection · chain E against E, 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 Q95VR4
Elsewhere: RCSB PDB 1PP7 · PDBe 1PP7 · UniProt Q95VR4

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