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Crystal structure of the T. vaginalis IBP39 initiator binding domain (ibd) bound to the alpha-scs inr element

Analyse Crystal structure of the T. vaginalis IBP39 initiator binding domain (ibd)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1PP8
Type: protein + DNA
Length: 751 residues
Chains: 14
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-scs inr; 39 kda initiator binding protein
UniProt: Q95VR4
Ligands: SO4
Pockets: 10 · best druggability 0.47

Structure

x-ray diffraction · 7 distinct chains · 47% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, I, Y, K	Alpha-scs inr	dna	12	—	—
T, R, J, G	Alpha-scs inr	dna	12	—	—
U	39 kda initiator binding protein	protein	111	50% helix, 12% strand	Q95VR4
P, M	39 kda initiator binding protein	protein	118	48% helix, 10% strand	Q95VR4
F	39 kda initiator binding protein	protein	113	47% helix, 14% strand	Q95VR4
V	39 kda initiator binding protein	protein	98	44% helix, 14% strand	Q95VR4
O	39 kda initiator binding protein	protein	97	42% helix, 11% strand	Q95VR4

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains V, O

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

Pockets

10 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	123	0.47	0.79	24	empty
2	92	0.41	0.78	19	empty
3	112	0.38	0.75	21	empty
4	69	0.37	0.78	15	empty
5	63	0.34	0.77	13	empty

Interfaces

29 interfaces between chains.

G–U · 558 Å² buried · 13 hydrogen bonds · protein-nucleic
K–F · 544 Å² buried · 9 hydrogen bonds · protein-nucleic
J–F · 534 Å² buried · 12 hydrogen bonds · protein-nucleic
Y–M · 517 Å² buried · 7 hydrogen bonds · protein-nucleic
R–M · 507 Å² buried · 6 hydrogen bonds · protein-nucleic

Compared structures

1PP8 · crystal structure of the T. vaginalis IBP39 Initiator binding domain (IBD) bound to the… · 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 1PP8 · PDBe 1PP8 · UniProt Q95VR4

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