MolNFT v1 · #167711 · protein

Naegleria gruberi RNA ligase D172A mutant apo

6VT1: “Naegleria gruberi RNA ligase D172A mutant apo”. X-ray diffraction, 1 ligand (AMP), 15 pockets (best druggability 0.81). MolNFT v1 #167711 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6VT1
Type: protein
Length: 1,356 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA ligase
UniProt: D2W2Z5
Ligands: AMP
Pockets: 15 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 20% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	RNA ligase	protein	339	20% helix, 35% strand	D2W2Z5

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D

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

Pockets

15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	759	0.81	0.84	68	AMP
2	769	0.80	0.83	68	AMP
3	876	0.80	0.82	78	AMP
4	847	0.78	0.81	70	AMP
5	960	0.75	0.78	97	empty

Interfaces

5 interfaces between chains.

A–D · 528 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 427 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 388 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 378 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 370 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6VT1 · Naegleria gruberi RNA ligase D172A mutant apo · 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 D2W2Z5
Elsewhere: RCSB PDB 6VT1 · PDBe 6VT1 · UniProt D2W2Z5

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