MolNFT v1 · #176395 · protein

The wild-type structure of 3,5-dahdhcca

7DL7 · 3,5-diaminohexanoate dehydrogenase: “The wild-type structure of 3,5-dahdhcca”. X-ray diffraction, 3 ligands (CA, CL, SO4), 20 pockets (best druggability 0.80). MolNFT v1 #176395 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 7DL7
Type: protein
Length: 2,803 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3,5-diaminohexanoate dehydrogenase
EC: 1.4.1.11
UniProt: B0VJ11
Ligands: CA, CL, SO4
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, H	3,5-diaminohexanoate dehydrogenase (EC 1.4.1.11)	protein	350	35% helix, 26% strand	B0VJ11
C, F, G	3,5-diaminohexanoate dehydrogenase (EC 1.4.1.11)	protein	351	34% helix, 25% strand	B0VJ11
E	3,5-diaminohexanoate dehydrogenase (EC 1.4.1.11)	protein	350	35% helix, 25% strand	B0VJ11

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains D, G
CL · Chloride ion · ion · 8 copies · chains A, F, C, D, E, G, H
SO4 · Sulfate ion · ion · 2 copies · chains B, F
EDO · 1,2-ethanediol · additive · 27 copies · chains A, D, B, C, H, E, F, G
PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, F, B, H, C
GOL · Glycerol · additive · chains D
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains 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, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1078	0.80	0.82	121	EDO
2	997	0.77	0.79	83	EDO
3	725	0.71	0.78	66	PEG
4	663	0.69	0.77	91	EDO, CA
5	563	0.67	0.77	49	EDO

Interfaces

12 interfaces between chains.

A–F · 2040 Å² buried · 25 hydrogen bonds · protein-protein
C–H · 1994 Å² buried · 28 hydrogen bonds · protein-protein
B–G · 1974 Å² buried · 24 hydrogen bonds · protein-protein
D–E · 1962 Å² buried · 27 hydrogen bonds · protein-protein
B–C · 434 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

7DL7 · The wild-type structure of 3,5-DAHDHcca · 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 B0VJ11
Elsewhere: RCSB PDB 7DL7 · PDBe 7DL7 · UniProt B0VJ11

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