MolNFT v1 · #99034 · protein

Structure of an enterococcus faecalis hd-domain protein complexed with dgtp and dttp

4LRL · Hd domain protein: “Structure of an enterococcus faecalis hd-domain protein complexed with dgtp and dttp”. X-ray diffraction, 3 ligands (DGT, TTP, NI), 20 pockets (best druggability 0.84). MolNFT v1 #99034 on GenesisL1: 3D…

PDB: 4LRL
Type: protein
Length: 1,790 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hd domain protein
UniProt: Q836G9
Ligands: DGT, TTP, NI
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 56% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hd domain protein	protein	451	56% helix, 12% strand	Q836G9
B	Hd domain protein	protein	445	55% helix, 12% strand	Q836G9
C	Hd domain protein	protein	455	56% helix, 12% strand	Q836G9
D	Hd domain protein	protein	439	56% helix, 11% strand	Q836G9

Ligands and binding sites

DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
TTP · Thymidine-5'-triphosphate · ligand · 2 copies · chains A, B, D, C
NI · Nickel (II) ion · metal · 4 copies · chains A, B, C, D
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, B
MLI · Malonate ion · additive · 2 copies · chains B, C

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	252	0.84	0.96	35	empty
2	254	0.84	0.96	37	empty
3	588	0.81	0.87	69	empty
4	1046	0.77	0.79	86	DGT, TTP
5	562	0.75	0.83	52	empty

Interfaces

6 interfaces between chains.

C–D · 2023 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1965 Å² buried · 21 hydrogen bonds · protein-protein
A–D · 946 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 919 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 872 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

4LRL · Structure of an Enterococcus Faecalis HD-domain protein complexed with dGTP and dTTP · 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 Q836G9
Elsewhere: RCSB PDB 4LRL · PDBe 4LRL · UniProt Q836G9

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