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Crystal structure of putative translation initiation inhibitor PH0854 from pyrococcus horikoshii

Analyse Crystal structure of putative translation initiation inhibitor PH0854 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2DYY
Type: protein
Length: 1,456 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: UPF0076 protein PH0854
UniProt: O58584
Pockets: 18 · best druggability 0.75

Structure

x-ray diffraction · 10 distinct chains · 26% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	UPF0076 protein PH0854	protein	125	27% helix, 32% strand	O58584
B, C, L	UPF0076 protein PH0854	protein	119	24% helix, 39% strand	O58584
D	UPF0076 protein PH0854	protein	126	27% helix, 33% strand	O58584
E	UPF0076 protein PH0854	protein	120	28% helix, 36% strand	O58584
F	UPF0076 protein PH0854	protein	118	23% helix, 34% strand	O58584
G	UPF0076 protein PH0854	protein	125	29% helix, 32% strand	O58584
H	UPF0076 protein PH0854	protein	122	20% helix, 34% strand	O58584
I	UPF0076 protein PH0854	protein	116	24% helix, 34% strand	O58584
J	UPF0076 protein PH0854	protein	124	28% helix, 33% strand	O58584
K	UPF0076 protein PH0854	protein	123	26% helix, 34% strand	O58584

Pockets

18 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	866	0.75	0.79	64	empty
2	710	0.75	0.80	81	empty
3	58	0.71	0.97	25	empty
4	229	0.68	0.85	37	empty
5	174	0.65	0.85	19	empty

Interfaces

19 interfaces between chains.

J–L · 1078 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 1057 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 1053 Å² buried · 13 hydrogen bonds · protein-protein
G–H · 1038 Å² buried · 10 hydrogen bonds · protein-protein
H–I · 1036 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

2DYY · Crystal structure of putative translation initiation inhibitor PH0854 from Pyrococcus… · the same entry in another collection · chain L against L, 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 O58584
Elsewhere: RCSB PDB 2DYY · PDBe 2DYY · UniProt O58584

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