MolNFT v1 · #137334 · protein

Crystal structure of medicago truncatula L-histidinol dehydrogenase in complex with L-histidinol

5VLC · Histidinol dehydrogenase, chloroplastic: “Crystal structure of medicago truncatula L-histidinol dehydrogenase in complex with L-histidinol”. X-ray diffraction, 2 ligands (HSO, ZN), 20 pockets (best druggability 0.86). MolNFT v1…

PDB: 5VLC
Type: protein
Length: 2,593 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histidinol dehydrogenase, chloroplastic
EC: 1.1.1.23
UniProt: G7IKX3
Ligands: HSO, ZN
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 4 distinct chains · 47% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histidinol dehydrogenase, chloroplastic (EC 1.1.1.23)	protein	431	47% helix, 16% strand	G7IKX3
B, D	Histidinol dehydrogenase, chloroplastic (EC 1.1.1.23)	protein	432	47% helix, 16% strand	G7IKX3
C, F	Histidinol dehydrogenase, chloroplastic (EC 1.1.1.23)	protein	434	47% helix, 16% strand	G7IKX3
E	Histidinol dehydrogenase, chloroplastic (EC 1.1.1.23)	protein	430	47% helix, 16% strand	G7IKX3

Ligands and binding sites

HSO · L-histidinol · ligand · 6 copies · chains A, B, C, D, E, F
ZN · Zinc ion · metal · 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, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1060	0.86	0.87	96	HSO
2	381	0.86	0.94	35	empty
3	381	0.85	0.94	36	empty
4	883	0.72	0.77	106	empty
5	434	0.70	0.81	49	HSO

Interfaces

14 interfaces between chains.

E–F · 5617 Å² buried · 108 hydrogen bonds · protein-protein
C–D · 5581 Å² buried · 100 hydrogen bonds · protein-protein
A–B · 5547 Å² buried · 100 hydrogen bonds · protein-protein
A–F · 450 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 410 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5VLC · Crystal Structure of Medicago truncatula L-Histidinol Dehydrogenase in Complex with… · 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 G7IKX3
Elsewhere: RCSB PDB 5VLC · PDBe 5VLC · UniProt G7IKX3

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