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Crystal structure of gida from chlorobium tepidum

Analyse Crystal structure of gida from chlorobium tepidum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3CP8
Type: protein
Length: 2,385 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRNA uridine 5-carboxymethylaminomethyl modification enzyme gida
EC: 1.-.-.-
UniProt: Q8KA85
Ligands: FAD
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	TRNA uridine 5-carboxymethylaminomethyl modification enzyme gida (EC 1.-.-.-)	protein	611	39% helix, 19% strand	Q8KA85
D	TRNA uridine 5-carboxymethylaminomethyl modification enzyme gida (EC 1.-.-.-)	protein	552	38% helix, 20% strand	Q8KA85

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	978	0.86	0.87	116	FAD
2	857	0.84	0.86	86	FAD
3	880	0.83	0.85	90	FAD
4	505	0.83	0.90	69	empty
5	498	0.83	0.90	65	empty

Interfaces

4 interfaces between chains.

C–D · 1814 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 1795 Å² buried · 26 hydrogen bonds · protein-protein
B–D · 196 Å² buried · 1 hydrogen bond · protein-protein
A–D · 64 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3CP8 · Crystal structure of GidA from Chlorobium tepidum · the same entry in another collection · chain A against A, TM-score 1.00
Q8KA85 · AlphaFold monomer V2.0 prediction for tRNA uridine 5-carboxymethylaminomethyl… · a predicted model of the same protein · chain D 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 Q8KA85
Elsewhere: RCSB PDB 3CP8 · PDBe 3CP8 · UniProt Q8KA85

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