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Crystal structure of TT0310 protein from thermus thermophilus HB8

Analyse Crystal structure of TT0310 protein 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: 1WM6
Type: protein
Length: 930 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phenylacetic acid degradation protein paai
UniProt: Q5SJP3
Ligands: CL
Pockets: 10 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 23% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, F	Phenylacetic acid degradation protein paai	protein	117	21% helix, 51% strand	Q5SJP3
B, H	Phenylacetic acid degradation protein paai	protein	116	24% helix, 50% strand	Q5SJP3
E, G	Phenylacetic acid degradation protein paai	protein	115	23% helix, 49% strand	Q5SJP3

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains A, B, C, D, E, F, G, H

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

Pockets

10 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	292	0.69	0.84	35	empty
2	229	0.69	0.85	36	empty
3	278	0.69	0.84	35	empty
4	264	0.68	0.84	33	empty
5	271	0.68	0.83	34	empty

Interfaces

14 interfaces between chains.

A–C · 1237 Å² buried · 20 hydrogen bonds · protein-protein
E–G · 1219 Å² buried · 23 hydrogen bonds · protein-protein
B–D · 1190 Å² buried · 23 hydrogen bonds · protein-protein
F–H · 1180 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 659 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1WM6 · Crystal structure of TT0310 protein from Thermus thermophilus HB8 · 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 Q5SJP3
Elsewhere: RCSB PDB 1WM6 · PDBe 1WM6 · UniProt Q5SJP3

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