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Crystal structure of K. polysporus DCR1 without the C-terminal dsrbd

Analyse Crystal structure of K. polysporus DCR1 without the C-terminal dsrbd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3RV0
Type: protein
Length: 1,003 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: K. polysporus DCR1
UniProt: A7TR32
Ligands: MG
Pockets: 20 · best druggability 0.56

Structure

x-ray diffraction · 4 distinct chains · 61% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	K. polysporus DCR1	protein	239	63% helix, 0% strand	A7TR32
B	K. polysporus DCR1	protein	304	60% helix, 6% strand	A7TR32
C	K. polysporus DCR1	protein	228	61% helix, 0% strand	A7TR32
D	K. polysporus DCR1	protein	232	62% helix, 0% strand	A7TR32

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	169	0.56	0.81	24	empty
2	176	0.55	0.80	25	empty
3	163	0.55	0.81	24	empty
4	120	0.54	0.83	20	empty
5	226	0.53	0.77	33	empty

Interfaces

4 interfaces between chains.

A–B · 6102 Å² buried · 70 hydrogen bonds · protein-protein
C–D · 5853 Å² buried · 61 hydrogen bonds · protein-protein
A–D · 501 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 190 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

3RV0 · Crystal structure of K. polysporus Dcr1 without the C-terminal dsRBD · 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 A7TR32
Elsewhere: RCSB PDB 3RV0 · PDBe 3RV0 · UniProt A7TR32

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