MolNFT v1 · #135449 · protein

Structure of the bldd CTD(D116A)-(C-di-GMP)2 intermediate, form 1

5TZF · DNA-binding protein: “Structure of the bldd CTD(D116A)-(C-di-GMP)2 intermediate, form 1”. X-ray diffraction, 1 ligand (C2E), 7 pockets (best druggability 0.74). MolNFT v1 #135449 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5TZF
Type: protein
Length: 616 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-binding protein
UniProt: F2RCL8
Ligands: C2E
Pockets: 7 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 55% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
J, I, N	DNA-binding protein	protein	78	55% helix, 12% strand	F2RCL8
B, H, M	DNA-binding protein	protein	76	57% helix, 11% strand	F2RCL8
E, D	DNA-binding protein	protein	77	55% helix, 10% strand	F2RCL8

Ligands and binding sites

C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · 8 copies · chains J, B, E, D, I, H, N, M

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	855	0.74	0.78	62	C2E
2	558	0.69	0.79	52	empty
3	329	0.51	0.73	31	C2E
4	147	0.50	0.79	18	empty
5	241	0.47	0.73	25	C2E

Interfaces

12 interfaces between chains.

J–M · 423 Å² buried · 2 hydrogen bonds · protein-protein
B–N · 336 Å² buried · 3 hydrogen bonds · protein-protein
E–H · 313 Å² buried · 3 hydrogen bonds · protein-protein
D–I · 297 Å² buried · 1 hydrogen bond · protein-protein
J–I · 192 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5TZF · Structure of the BldD CTD(D116A)-(c-di-GMP)2 intermediate, form 1 · the same entry in another collection · chain J against J, 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 F2RCL8
Elsewhere: RCSB PDB 5TZF · PDBe 5TZF · UniProt F2RCL8

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