MolNFT v1 · #88322 · protein

Crystal structure of the N-acetyl-D-mannosamine dehydrogenase with N- acetylmannosamine

4CR7 · N-acylmannosamine 1-dehydrogenase: “Crystal structure of the N-acetyl-D-mannosamine dehydrogenase with N- acetylmannosamine”. X-ray diffraction, 2 ligands (BM3, MAN), 20 pockets (best druggability 0.71). MolNFT v1 #88322 on…

PDB: 4CR7
Type: protein
Length: 4,147 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: N-acylmannosamine 1-dehydrogenase
EC: 1.1.1.233
UniProt: P22441
Ligands: BM3, MAN
Pockets: 20 · best druggability 0.71

Structure

x-ray diffraction · 7 distinct chains · 46% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, J, K, M, N, O, P	N-acylmannosamine 1-dehydrogenase (EC 1.1.1.233)	protein	260	47% helix, 15% strand	P22441
C, D	N-acylmannosamine 1-dehydrogenase (EC 1.1.1.233)	protein	257	47% helix, 15% strand	P22441
E, F	N-acylmannosamine 1-dehydrogenase (EC 1.1.1.233)	protein	259	46% helix, 15% strand	P22441
G	N-acylmannosamine 1-dehydrogenase (EC 1.1.1.233)	protein	258	45% helix, 15% strand	P22441
H	N-acylmannosamine 1-dehydrogenase (EC 1.1.1.233)	protein	257	47% helix, 15% strand	P22441
I	N-acylmannosamine 1-dehydrogenase (EC 1.1.1.233)	protein	261	46% helix, 15% strand	P22441
L	N-acylmannosamine 1-dehydrogenase (EC 1.1.1.233)	protein	259	47% helix, 15% strand	P22441

Ligands and binding sites

BM3 · 2-acetamido-2-deoxy-alpha-D-mannopyranose · ligand · 16 copies · chains A, B, M, C, D, E, F, G, H, I, J, K, L, N, O, P
MAN · alpha-D-mannopyranose · sugar · 4 copies · chains D, B, M, N, P
PG4 · Tetraethylene glycol · additive · 14 copies · chains A, B, M, E, D, F, G, H, I, J, K, P

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	601	0.71	0.79	47	empty
2	701	0.70	0.77	70	BM3
3	517	0.70	0.79	57	PG4, BM3
4	574	0.69	0.78	63	PG4, BM3
5	437	0.69	0.80	49	PG4, BM3

Interfaces

21 interfaces between chains.

B–L · 1847 Å² buried · 28 hydrogen bonds · protein-protein
A–K · 1846 Å² buried · 25 hydrogen bonds · protein-protein
D–F · 1580 Å² buried · 7 hydrogen bonds · protein-protein
I–O · 1579 Å² buried · 11 hydrogen bonds · protein-protein
L–M · 1576 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 glycan (glycosylation).

Compared structures

4CR7 · Crystal structure of the N-acetyl-D-mannosamine dehydrogenase with n-acetylmannosamine · the same entry in another collection · chain K against K, 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 P22441
Elsewhere: RCSB PDB 4CR7 · PDBe 4CR7 · UniProt P22441

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