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Crystal structure of native TTHA0252 from thermus thermophilus HB8

Analyse Crystal structure of native TTHA0252 from thermus thermophilus HB8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3IEK
Type: protein
Length: 1,724 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease TTHA0252
EC: 3.1.-.-
UniProt: Q5SLP1
Ligands: ZN, SO4
Pockets: 15 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Ribonuclease TTHA0252 (EC 3.1.-.-)	protein	431	35% helix, 22% strand	Q5SLP1

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 100 copies · chains A, D, B, C
FLC · Citrate anion · additive · 2 copies · chains A, B

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

Pockets

15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	895	0.79	0.82	86	SO4
2	936	0.79	0.81	78	SO4
3	815	0.78	0.82	66	SO4
4	824	0.78	0.81	71	SO4
5	548	0.74	0.82	60	SO4

Interfaces

3 interfaces between chains.

A–D · 1186 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 1104 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 766 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

3IEK · Crystal Structure of native TTHA0252 from Thermus thermophilus HB8 · the same entry in another collection · chain A against A, TM-score 1.00
Q5SLP1 · AlphaFold monomer V2.0 prediction for ribonuclease TTHA0252 (Q5SLP1) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q5SLP1
Elsewhere: RCSB PDB 3IEK · PDBe 3IEK · UniProt Q5SLP1

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