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Crystal structure of rice GID1 complexed with GA3

Analyse Crystal structure of rice GID1 complexed with GA3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ED1
Type: protein
Length: 1,871 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gibberellin receptor GID1
EC: 3.-.-.-
UniProt: Q6L545
Ligands: GA3, NO3, PO4
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 6 distinct chains · 38% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gibberellin receptor GID1 (EC 3.-.-.-)	protein	321	39% helix, 19% strand	Q6L545
B	Gibberellin receptor GID1 (EC 3.-.-.-)	protein	316	38% helix, 18% strand	Q6L545
C	Gibberellin receptor GID1 (EC 3.-.-.-)	protein	301	40% helix, 19% strand	Q6L545
D	Gibberellin receptor GID1 (EC 3.-.-.-)	protein	315	38% helix, 19% strand	Q6L545
E	Gibberellin receptor GID1 (EC 3.-.-.-)	protein	313	37% helix, 20% strand	Q6L545
F	Gibberellin receptor GID1 (EC 3.-.-.-)	protein	305	39% helix, 19% strand	Q6L545

Ligands and binding sites

GA3 · Gibberellin A3 · ligand · 6 copies · chains A, B, C, D, E, F
NO3 · Nitrate ion · ion · 12 copies · chains A, B, C, D, F, E
PO4 · Phosphate ion · ion · 2 copies · chains A, B, E, F
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 6 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	233	0.84	0.96	34	GA3
2	245	0.83	0.95	34	GA3
3	233	0.83	0.96	35	GA3
4	240	0.83	0.95	34	GA3
5	254	0.83	0.95	42	GA3

Interfaces

7 interfaces between chains.

E–F · 955 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 953 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 952 Å² buried · 7 hydrogen bonds · protein-protein
B–E · 257 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 252 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3ED1 · Crystal Structure of Rice GID1 complexed with GA3 · the same entry in another collection · chain F against F, TM-score 1.00
Q6L545 · AlphaFold monomer V2.0 prediction for gibberellin receptor GID1 (Q6L545) · 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 Q6L545
Elsewhere: RCSB PDB 3ED1 · PDBe 3ED1 · UniProt Q6L545

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