MolNFT v1 · #147353 · protein

Pseudomonas syringae selo

6EAC: “Pseudomonas syringae selo”. X-ray diffraction, 4 ligands (ANP, CA, MG), 20 pockets (best druggability 0.81). MolNFT v1 #147353 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6EAC
Type: protein
Length: 1,902 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Selo
EC: 2.7.7.-
UniProt: Q87VB1
Ligands: ANP, CA, MG, CL
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Selo (EC 2.7.7.-)	protein	476	46% helix, 14% strand	Q87VB1
C, D	Selo (EC 2.7.7.-)	protein	475	47% helix, 14% strand	Q87VB1

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 14 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
CL · Chloride ion · ion · 4 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 21 copies · chains A, B, C, D
PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B, C, D
ACT · Acetate ion · additive · 4 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	743	0.81	0.85	81	MG, CA, CL, ANP
2	637	0.79	0.85	69	MG, CA, CL, ANP
3	419	0.64	0.78	52	EDO
4	402	0.62	0.78	45	MG, CA, ANP
5	406	0.61	0.77	38	MG, CA, CL, ANP

Interfaces

5 interfaces between chains.

A–B · 724 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 509 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 490 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 431 Å² buried · 1 hydrogen bond · protein-protein
A–D · 340 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6EAC · Pseudomonas syringae SelO · the same entry in another collection · chain A against A, TM-score 1.00
Q87VB1 · AlphaFold monomer V2.0 prediction for protein adenylyltransferase selo (Q87VB1) · a predicted model of the same protein · chain C 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 Q87VB1
Elsewhere: RCSB PDB 6EAC · PDBe 6EAC · UniProt Q87VB1

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