MolNFT v1 · #65241 · protein

Crystal structure of cold H188K S187N

3GR9: “Crystal structure of cold H188K S187N”. X-ray diffraction, 1 ligand (AKG), 20 pockets (best druggability 0.75). MolNFT v1 #65241 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3GR9
Type: protein
Length: 3,075 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cold
UniProt: Q9F118
Ligands: AKG
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 7 distinct chains · 38% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cold	protein	384	39% helix, 19% strand	Q9F118
B	Cold	protein	385	38% helix, 19% strand	Q9F118
C	Cold	protein	388	37% helix, 18% strand	Q9F118
D, H	Cold	protein	381	38% helix, 18% strand	Q9F118
E	Cold	protein	383	39% helix, 18% strand	Q9F118
F	Cold	protein	386	38% helix, 18% strand	Q9F118
G	Cold	protein	387	38% helix, 19% strand	Q9F118

Ligands and binding sites

AKG · 2-oxoglutaric acid · ligand · 6 copies · chains A, B, C, D, E, F, G, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	82	0.75	0.98	24	empty
2	72	0.74	0.98	20	empty
3	70	0.73	0.98	25	empty
4	942	0.73	0.77	91	empty
5	61	0.71	0.98	25	empty

Interfaces

11 interfaces between chains.

C–D · 2624 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 2623 Å² buried · 25 hydrogen bonds · protein-protein
G–H · 2618 Å² buried · 25 hydrogen bonds · protein-protein
E–F · 2567 Å² buried · 27 hydrogen bonds · protein-protein
A–C · 342 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (cofactor).

Compared structures

3GR9 · Crystal structure of ColD H188K S187N · the same entry in another collection · chain A 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 Q9F118
Elsewhere: RCSB PDB 3GR9 · PDBe 3GR9 · UniProt Q9F118

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