MolNFT v1 · #153986 · protein

Crystal structure of egoc

6JWP · GTP-binding protein GTR1: “Crystal structure of egoc”. X-ray diffraction, 2 ligands (GNP, MG), 20 pockets (best druggability 0.66). MolNFT v1 #153986 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6JWP
Type: protein
Length: 1,671 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTP-binding protein GTR1; GTP-binding protein GTR2; Protein MEH1; EGO2; Protein SLM4
UniProt: Q00582, P53290, Q02205, Q3E830, P38247
Ligands: GNP, MG
Pockets: 20 · best druggability 0.66

Structure

x-ray diffraction · 10 distinct chains · 39% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GTP-binding protein GTR1	protein	275	43% helix, 23% strand	Q00582
B	GTP-binding protein GTR2	protein	294	42% helix, 21% strand	P53290
C	Protein MEH1	protein	100	59% helix, 8% strand	Q02205
D	EGO2	protein	67	15% helix, 48% strand	Q3E830
E	Protein SLM4	protein	146	31% helix, 32% strand	P38247
F	GTP-binding protein GTR1	protein	289	39% helix, 22% strand	Q00582
G	GTP-binding protein GTR2	protein	197	41% helix, 16% strand	P53290
H	Protein MEH1	protein	94	57% helix, 5% strand	Q02205
I	EGO2	protein	65	14% helix, 45% strand	Q3E830
J	Protein SLM4	protein	144	31% helix, 34% strand	P38247

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 3 copies · chains A, B, F
MG · Magnesium ion · metal · 3 copies · chains A, B, 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, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	235	0.66	0.84	27	empty
2	195	0.60	0.81	25	empty
3	439	0.58	0.75	35	empty
4	232	0.58	0.79	27	empty
5	122	0.55	0.82	24	empty

Interfaces

17 interfaces between chains.

H–J · 1853 Å² buried · 26 hydrogen bonds · protein-protein
C–E · 1842 Å² buried · 31 hydrogen bonds · protein-protein
F–G · 1460 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 1436 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 1379 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

6JWP · crystal structure of EGOC · the same entry in another collection · chain J against J, TM-score 1.00
Q00582 · AlphaFold monomer V2.0 prediction for GTP-binding protein GTR1 (Q00582) · a predicted model of the same protein · chain F against A, TM-score 0.99

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 Q00582
Every structure of UniProt P53290
Every structure of UniProt Q02205
Every structure of UniProt Q3E830
Every structure of UniProt P38247
Elsewhere: RCSB PDB 6JWP · PDBe 6JWP · UniProt Q00582 · UniProt P53290 · UniProt Q02205 · UniProt Q3E830 · UniProt P38247

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