MolNFT v1 · #57008 · protein

Structure of aquifex aeolicus gida in the form I crystal

2ZXH · TRNA uridine 5-carboxymethylaminomethyl modification enzyme…: “Structure of aquifex aeolicus gida in the form I crystal”. X-ray diffraction, 2 ligands (FAD, PO4), 14 pockets (best druggability 0.89). MolNFT v1 #57008 on GenesisL1…

PDB: 2ZXH
Type: protein
Length: 1,204 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmg
UniProt: O66962
Ligands: FAD, PO4
Pockets: 14 · best druggability 0.89

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	TRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmg	protein	603	36% helix, 19% strand	O66962
B	TRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmg	protein	601	37% helix, 19% strand	O66962

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 3 copies · chains A, B

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

Pockets

14 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	1000	0.89	0.91	144	FAD
2	867	0.84	0.87	82	FAD
3	504	0.74	0.83	47	PO4
4	495	0.74	0.82	45	PO4
5	123	0.73	0.93	31	empty

Interfaces

1 interface between chains.

A–B · 2391 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

2ZXH · Structure of Aquifex aeolicus GidA in the form I crystal · the same entry in another collection · chain A against A, TM-score 1.00
O66962 · AlphaFold monomer V2.0 prediction for tRNA uridine 5-carboxymethylaminomethyl… · a predicted model of the same protein · chain B against A, TM-score 0.98

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 O66962
Elsewhere: RCSB PDB 2ZXH · PDBe 2ZXH · UniProt O66962

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