MolNFT v1 · #167725 · protein

Naegleria gruberi RNA ligase E227A mutant apo

6VTG: “Naegleria gruberi RNA ligase E227A mutant apo”. X-ray diffraction, 18 pockets (best druggability 0.83). MolNFT v1 #167725 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6VTG
Type: protein
Length: 1,360 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA ligase
UniProt: D2W2Z5
Pockets: 18 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 20% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	RNA ligase	protein	340	20% helix, 36% strand	D2W2Z5

Pockets

18 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	1153	0.83	0.84	108	empty
2	842	0.79	0.82	77	empty
3	843	0.79	0.82	75	empty
4	762	0.78	0.82	63	empty
5	447	0.72	0.82	53	empty

Interfaces

5 interfaces between chains.

B–C · 609 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 489 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 444 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 402 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 400 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6VTG · Naegleria gruberi RNA ligase E227A 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 6VTG · PDBe 6VTG · UniProt D2W2Z5

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