MolNFT v1 · #101512 · protein

E.COLI qued, semet protein, 2A resolution

4NTN · 6-carboxy-5,6,7,8-tetrahydropterin synthase: “E.COLI qued, semet protein, 2A resolution”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.77). MolNFT v1 #101512 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4NTN
Type: protein
Length: 710 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 6-carboxy-5,6,7,8-tetrahydropterin synthase
EC: 4.1.2.50
UniProt: P65870
Ligands: ZN
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 5 distinct chains · 28% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	6-carboxy-5,6,7,8-tetrahydropterin synthase (EC 4.1.2.50)	protein	118	28% helix, 34% strand	P65870
B, D	6-carboxy-5,6,7,8-tetrahydropterin synthase (EC 4.1.2.50)	protein	119	28% helix, 34% strand	P65870
C	6-carboxy-5,6,7,8-tetrahydropterin synthase (EC 4.1.2.50)	protein	117	28% helix, 34% strand	P65870
E	6-carboxy-5,6,7,8-tetrahydropterin synthase (EC 4.1.2.50)	protein	119	28% helix, 34% strand	P65870
F	6-carboxy-5,6,7,8-tetrahydropterin synthase (EC 4.1.2.50)	protein	118	28% helix, 31% strand	P65870

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
FMT · Formic acid · additive · chains A

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	1062	0.77	0.79	112	empty
2	646	0.74	0.81	76	ZN
3	484	0.72	0.81	62	ZN
4	394	0.65	0.79	33	empty
5	120	0.44	0.77	17	empty

Interfaces

9 interfaces between chains.

A–B · 780 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 758 Å² buried · 22 hydrogen bonds · protein-protein
B–E · 756 Å² buried · 14 hydrogen bonds · protein-protein
A–E · 751 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 743 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 modified (engineered).

Compared structures

4NTN · E.coli QueD, SeMet protein, 2A resolution · the same entry in another collection · chain F against F, TM-score 1.00
P65870 · AlphaFold monomer V2.0 prediction for 6-carboxy-5,6,7,8-tetrahydropterin synthase (P65870) · 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 P65870
Elsewhere: RCSB PDB 4NTN · PDBe 4NTN · UniProt P65870

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