MolNFT v1 · #74598 · protein

Crystal structure of human GTPase imap family member 2 in the nucleotide-free state

3P1J: “Crystal structure of human GTPase imap family member 2 in the nucleotide-free state”. X-ray diffraction, 1 ligand (UNX), 4 pockets (best druggability 0.51). MolNFT v1 #74598 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 3P1J
Type: protein
Length: 749 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTPase imap family member 2
UniProt: Q9UG22
Ligands: UNX
Pockets: 4 · best druggability 0.51

Structure

x-ray diffraction · 4 distinct chains · 50% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GTPase imap family member 2	protein	190	48% helix, 21% strand	Q9UG22
B	GTPase imap family member 2	protein	180	52% helix, 18% strand	Q9UG22
C	GTPase imap family member 2	protein	186	51% helix, 21% strand	Q9UG22
D	GTPase imap family member 2	protein	193	47% helix, 19% strand	Q9UG22

Ligands and binding sites

UNX · Unknown atom or ion · ion · 19 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	175	0.51	0.78	29	empty
2	78	0.48	0.82	18	empty
3	132	0.44	0.77	22	empty
4	70	0.39	0.78	20	empty

Interfaces

4 interfaces between chains.

A–D · 878 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 756 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 410 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 23 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3P1J · Crystal structure of human GTPase IMAP family member 2 in the nucleotide-free state · the same entry in another collection · chain D against D, TM-score 1.00
Q9UG22 · AlphaFold monomer V2.0 prediction for GTPase imap family member 2 (Q9UG22) · 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 Q9UG22
Elsewhere: RCSB PDB 3P1J · PDBe 3P1J · UniProt Q9UG22

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