MolNFT v1 · #116043 · protein

Archaeal ATP-dependent RNA ligase - form 2

5D1P: “Archaeal ATP-dependent RNA ligase - form 2”. X-ray diffraction, 2 ligands (MG, SO4), 5 pockets (best druggability 0.63). MolNFT v1 #116043 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5D1P
Type: protein
Length: 750 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP-dependent RNA ligase
UniProt: O27289
Ligands: MG, SO4
Pockets: 5 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	ATP-dependent RNA ligase	protein	375	38% helix, 26% strand	O27289

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 6 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	489	0.63	0.76	45	SO4, MG
2	510	0.60	0.74	47	SO4, MG
3	118	0.53	0.82	15	empty
4	94	0.51	0.83	15	empty
5	59	0.29	0.74	16	empty

Interfaces

1 interface between chains.

A–B · 2294 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (nonstandard).

Compared structures

5D1P · Archaeal ATP-dependent RNA ligase - form 2 · 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 O27289
Elsewhere: RCSB PDB 5D1P · PDBe 5D1P · UniProt O27289

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