MolNFT v1 · #69118 · protein

Crystal structure of E. COLI RNA 3' cyclase

3KGD · RNA 3'-terminal phosphate cyclase: “Crystal structure of E. COLI RNA 3' cyclase”. X-ray diffraction, 3 ligands (AMP, NA, SO4), 20 pockets (best druggability 0.82). MolNFT v1 #69118 on GenesisL1: 3D structure, binding sites and…

PDB: 3KGD
Type: protein
Length: 1,356 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA 3'-terminal phosphate cyclase
EC: 6.5.1.4
UniProt: P46849
Ligands: AMP, NA, SO4
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA 3'-terminal phosphate cyclase (EC 6.5.1.4)	protein	336	33% helix, 31% strand	P46849
B	RNA 3'-terminal phosphate cyclase (EC 6.5.1.4)	protein	342	32% helix, 30% strand	P46849
C	RNA 3'-terminal phosphate cyclase (EC 6.5.1.4)	protein	338	34% helix, 30% strand	P46849
D	RNA 3'-terminal phosphate cyclase (EC 6.5.1.4)	protein	340	33% helix, 29% strand	P46849

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
NA · Sodium ion · metal · 5 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
GOL · Glycerol · additive · 10 copies · chains A, C, B, 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, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	958	0.82	0.83	101	GOL
2	935	0.79	0.82	118	AMP, GOL, NA, SO4
3	100	0.78	0.98	26	empty
4	86	0.77	0.99	24	empty
5	85	0.76	0.98	22	empty

Interfaces

5 interfaces between chains.

A–B · 499 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 372 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 322 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 314 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 15 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

3KGD · Crystal structure of E. coli RNA 3' cyclase · the same entry in another collection · chain D against D, TM-score 1.00
P46849 · AlphaFold monomer V2.0 prediction for RNA 3'-terminal phosphate cyclase (P46849) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P46849
Elsewhere: RCSB PDB 3KGD · PDBe 3KGD · UniProt P46849

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