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Crystal structure of the 1L-myo-INOSITOL/NAD+ complex

Analyse Crystal structure of the 1L-myo-INOSITOL/NAD+ complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1P1H
Type: protein
Length: 2,001 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Inositol-3-phosphate synthase
EC: 5.5.1.4
UniProt: P11986
Ligands: NAD
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Inositol-3-phosphate synthase (EC 5.5.1.4)	protein	506	33% helix, 26% strand	P11986
B	Inositol-3-phosphate synthase (EC 5.5.1.4)	protein	491	32% helix, 26% strand	P11986
C	Inositol-3-phosphate synthase (EC 5.5.1.4)	protein	517	35% helix, 24% strand	P11986
D	Inositol-3-phosphate synthase (EC 5.5.1.4)	protein	487	33% helix, 26% strand	P11986

Ligands and binding sites

NAD · Nicotinamide-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	383	0.87	0.96	79	NAD
2	646	0.84	0.88	102	NAD
3	786	0.83	0.86	95	empty
4	546	0.83	0.89	56	empty
5	582	0.83	0.88	73	empty

Interfaces

6 interfaces between chains.

C–D · 5918 Å² buried · 74 hydrogen bonds · protein-protein
A–B · 5878 Å² buried · 78 hydrogen bonds · protein-protein
A–C · 1011 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 636 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 567 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1P1H · Crystal structure of the 1L-myo-inositol/NAD+ complex · the same entry in another collection · chain D against D, TM-score 1.00
P11986 · AlphaFold monomer V2.0 prediction for inositol-3-phosphate synthase (P11986) · a predicted model of the same protein · chain B 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 P11986
Elsewhere: RCSB PDB 1P1H · PDBe 1P1H · UniProt P11986

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