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Structure of a natural red emitting luciferase from phrixothrix hirtus (P1 crystal form)

Analyse Structure of a natural red emitting luciferase from phrixothrix hirtus (P1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ABH
Type: protein
Length: 3,249 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Red-bioluminescence eliciting luciferase
UniProt: Q9U4U7
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 8 distinct chains · 31% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Red-bioluminescence eliciting luciferase	protein	377	35% helix, 16% strand	Q9U4U7
B	Red-bioluminescence eliciting luciferase	protein	405	32% helix, 15% strand	Q9U4U7
C	Red-bioluminescence eliciting luciferase	protein	409	31% helix, 15% strand	Q9U4U7
D	Red-bioluminescence eliciting luciferase	protein	442	29% helix, 18% strand	Q9U4U7
E	Red-bioluminescence eliciting luciferase	protein	398	31% helix, 15% strand	Q9U4U7
F	Red-bioluminescence eliciting luciferase	protein	417	30% helix, 17% strand	Q9U4U7
G	Red-bioluminescence eliciting luciferase	protein	401	32% helix, 15% strand	Q9U4U7
H	Red-bioluminescence eliciting luciferase	protein	400	33% helix, 15% strand	Q9U4U7

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1120	0.87	0.88	104	empty
2	818	0.84	0.86	56	empty
3	814	0.83	0.86	57	empty
4	905	0.83	0.85	69	empty
5	522	0.81	0.88	63	empty

Interfaces

16 interfaces between chains.

D–F · 1061 Å² buried · 18 hydrogen bonds · protein-protein
C–E · 977 Å² buried · 15 hydrogen bonds · protein-protein
A–G · 972 Å² buried · 16 hydrogen bonds · protein-protein
B–H · 937 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 566 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6ABH · Structure of a natural red emitting luciferase from Phrixothrix hirtus (P1 crystal form) · 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 Q9U4U7
Elsewhere: RCSB PDB 6ABH · PDBe 6ABH · UniProt Q9U4U7

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