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Crystal structure of full-length thermus thermophilus carh bound to adenosylcobalamin (dark state)

Analyse Crystal structure of full-length thermus thermophilus carh bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5C8D
Type: protein
Length: 2,026 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Light-dependent transcriptional regulator carh
UniProt: Q746J7
Ligands: B12, 5AD
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 8 distinct chains · 57% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Light-dependent transcriptional regulator carh	protein	219	58% helix, 8% strand	Q746J7
B	Light-dependent transcriptional regulator carh	protein	221	58% helix, 8% strand	Q746J7
C	Light-dependent transcriptional regulator carh	protein	223	58% helix, 8% strand	Q746J7
D	Light-dependent transcriptional regulator carh	protein	273	57% helix, 10% strand	Q746J7
E	Light-dependent transcriptional regulator carh	protein	280	55% helix, 9% strand	Q746J7
F	Light-dependent transcriptional regulator carh	protein	270	58% helix, 9% strand	Q746J7
G	Light-dependent transcriptional regulator carh	protein	263	59% helix, 7% strand	Q746J7
H	Light-dependent transcriptional regulator carh	protein	277	56% helix, 9% strand	Q746J7

Ligands and binding sites

B12 · Cobalamin · ligand · 8 copies · chains A, B, C, D, E, F, G, H
5AD · 5'-deoxyadenosine · ligand · 8 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

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	288	0.85	0.96	55	empty
2	245	0.84	0.96	37	empty
3	1075	0.81	0.82	94	B12
4	757	0.78	0.82	83	B12
5	998	0.78	0.80	87	B12, 5AD

Interfaces

14 interfaces between chains.

C–D · 1451 Å² buried · 26 hydrogen bonds · protein-protein
E–F · 1448 Å² buried · 26 hydrogen bonds · protein-protein
G–H · 1441 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 1439 Å² buried · 27 hydrogen bonds · protein-protein
E–H · 988 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5C8D · Crystal structure of full-length Thermus thermophilus CarH bound to adenosylcobalamin… · the same entry in another collection · chain H against H, 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 Q746J7
Elsewhere: RCSB PDB 5C8D · PDBe 5C8D · UniProt Q746J7

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