MolNFT v1 · #26373 · protein

Crystal structure of TT0310 protein from thermus thermophilus HB8

1WN3 · Phenylacetic acid degradation protein paai: “Crystal structure of TT0310 protein from thermus thermophilus HB8”. X-ray diffraction, 2 ligands (HXC, CL), 8 pockets (best druggability 0.77). MolNFT v1 #26373 on GenesisL1: 3D…

PDB: 1WN3
Type: protein
Length: 926 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phenylacetic acid degradation protein paai
UniProt: Q5SJP3
Ligands: HXC, CL
Pockets: 8 · best druggability 0.77

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, F	Phenylacetic acid degradation protein paai	protein	116	23% helix, 50% strand	Q5SJP3
C, E, G	Phenylacetic acid degradation protein paai	protein	115	22% helix, 50% strand	Q5SJP3
H	Phenylacetic acid degradation protein paai	protein	117	24% helix, 50% strand	Q5SJP3

Ligands and binding sites

HXC · Hexanoyl-coenzyme A · ligand · 4 copies · chains A, C, D, H, B, E, G, F
CL · Chloride ion · ion · 2 copies · chains A, B, C, D, E, F, G, H
ACT · Acetate ion · additive · chains E, G

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

Pockets

8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	875	0.77	0.80	84	HXC
2	260	0.68	0.84	32	HXC
3	267	0.67	0.83	36	empty
4	277	0.67	0.82	33	empty
5	226	0.67	0.84	34	empty

Interfaces

16 interfaces between chains.

F–H · 1300 Å² buried · 27 hydrogen bonds · protein-protein
E–G · 1273 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 1246 Å² buried · 29 hydrogen bonds · protein-protein
B–D · 1237 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 621 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

1WN3 · 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 1WN3 · PDBe 1WN3 · UniProt Q5SJP3

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