MolNFT v1 · #80336 · protein

Crystal structure of leuconostoc mesenteroides nrrl B-1299 N- terminally truncated dextransucrase dsr-E in triclinic form

3TTO: “Crystal structure of leuconostoc mesenteroides nrrl B-1299 N- terminally truncated dextransucrase dsr-E in…”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.79). MolNFT v1 #80336 on GenesisL1: 3D structure…

PDB: 3TTO
Type: protein
Length: 4,203 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dextransucrase
EC: 2.4.1.5
UniProt: Q8G9Q2
Ligands: CA
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 22% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dextransucrase (EC 2.4.1.5)	protein	1055	22% helix, 25% strand	Q8G9Q2
B	Dextransucrase (EC 2.4.1.5)	protein	1053	21% helix, 27% strand	Q8G9Q2
C	Dextransucrase (EC 2.4.1.5)	protein	1052	22% helix, 26% strand	Q8G9Q2
D	Dextransucrase (EC 2.4.1.5)	protein	1043	23% helix, 23% strand	Q8G9Q2

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 9 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1152	0.79	0.80	89	empty
2	564	0.77	0.83	57	empty
3	765	0.73	0.79	59	empty
4	971	0.71	0.76	100	empty
5	281	0.71	0.85	34	empty

Interfaces

5 interfaces between chains.

A–B · 703 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 435 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 434 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 402 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 148 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3TTO · Crystal structure of Leuconostoc mesenteroides NRRL B-1299 N-terminally truncated… · 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 Q8G9Q2
Elsewhere: RCSB PDB 3TTO · PDBe 3TTO · UniProt Q8G9Q2

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