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Crystal structure of a putative nucleoside deoxyribosyltransferase (BDI_0649) from parabacteroides distasonis atcc 8503 at 2.40 a resolution

Analyse Crystal structure of a putative nucleoside deoxyribosyltransferase (BDI_0649)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4MCJ
Type: protein
Length: 1,510 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein
UniProt: A6L9R1
Ligands: CL
Pockets: 10 · best druggability 0.73

Structure

x-ray diffraction · 8 distinct chains · 38% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Uncharacterized protein	protein	150	38% helix, 20% strand	A6L9R1
B, F	Uncharacterized protein	protein	152	38% helix, 20% strand	A6L9R1
C	Uncharacterized protein	protein	152	38% helix, 20% strand	A6L9R1
E	Uncharacterized protein	protein	149	38% helix, 20% strand	A6L9R1
G	Uncharacterized protein	protein	154	37% helix, 19% strand	A6L9R1
H	Uncharacterized protein	protein	149	38% helix, 20% strand	A6L9R1
I	Uncharacterized protein	protein	149	38% helix, 20% strand	A6L9R1
J	Uncharacterized protein	protein	153	38% helix, 20% strand	A6L9R1

Ligands and binding sites

CL · Chloride ion · ion · 9 copies · chains A, B, C, D, F, G, H, I, J

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

Pockets

10 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	937	0.73	0.77	83	empty
2	729	0.72	0.78	80	CL
3	720	0.72	0.78	79	CL
4	508	0.63	0.76	43	empty
5	261	0.60	0.80	26	CL

Interfaces

16 interfaces between chains.

G–H · 1354 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 1340 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1332 Å² buried · 13 hydrogen bonds · protein-protein
I–J · 1327 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 1317 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 69 modified (engineered).

Compared structures

4MCJ · Crystal structure of a putative nucleoside deoxyribosyltransferase (BDI_0649) from… · 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 A6L9R1
Elsewhere: RCSB PDB 4MCJ · PDBe 4MCJ · UniProt A6L9R1

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