SMTL ID : 4cr7.7 (8 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

6 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.1: 5 residues within 4Å: Chain A: E.160, P.161 Chain D: M.266, R.271 Ligands: BM3.2 No protein-ligand interaction detected (PLIP) PG4.6: 9 residues within 4Å: Chain C: F.157, T.253, S.259 Chain D: F.157, R.178, T.251, T.253, S.259 Ligands: PG4.10 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:R.178, C:S.259, C:S.259, D:R.178, D:R.178, D:T.253, D:S.259, D:S.259 Water bridges: C:T.253 PG4.7: 7 residues within 4Å: Chain B: S.156, F.157, M.175 Chain D: S.156, F.157, M.175, R.178 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.178 PG4.8: 7 residues within 4Å: Chain A: M.266, R.271 Chain D: E.160, P.161, E.162, L.213 Ligands: BM3.9 1 PLIP interactions: 1 interactions with chain D Water bridges: D:E.160 PG4.10: 5 residues within 4Å: Chain A: R.178 Chain B: F.157, T.253, S.259 Ligands: PG4.6 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.259, A:R.178, A:R.178 Water bridges: B:T.251, B:T.251 PG4.11: 3 residues within 4Å: Chain A: T.253, S.259 Chain B: R.178 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.253, A:T.253, A:S.259, B:R.178, B:R.178

4 x BM3: 2-acetamido-2-deoxy-alpha-D-mannopyranose(Non-covalent)

BM3.2: 12 residues within 4Å: Chain A: K.98, G.99, S.153, N.155, E.160, A.163, Y.166, P.196, G.197, P.198, Y.208 Ligands: PG4.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.163, A:Y.166 Hydrogen bonds: A:G.99, A:N.155, A:E.160, A:Y.208 BM3.3: 10 residues within 4Å: Chain B: K.98, G.99, S.153, N.155, E.160, Y.166, G.197, P.198, Y.208 Chain C: I.262 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.166 Hydrogen bonds: B:G.99, B:N.155, B:E.160, B:Y.166, B:Y.208 BM3.4: 11 residues within 4Å: Chain B: I.262, F.263 Chain C: K.98, G.99, S.153, N.155, E.160, Y.166, G.197, P.198, Y.208 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.166 Hydrogen bonds: C:G.99, C:S.153, C:N.155, C:E.160 BM3.9: 11 residues within 4Å: Chain A: F.263 Chain D: K.98, G.99, S.153, N.155, E.160, Y.166, G.197, P.198, Y.208 Ligands: PG4.8 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.99, D:N.155, D:E.160, D:Y.166

1 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.5: 12 residues within 4Å: Chain B: M.158, E.220, L.258, S.259, M.261, I.262 Chain C: M.158, E.220, L.258, S.259, M.261, I.262 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:L.258, B:M.261, C:E.220, C:M.261

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sola-Carvajal, A. et al., Crystal Structures and Functional Studies Clarify Substrate Selectivity and Catalytic Residues for the Unique Orphan Enzyme N-Acetyl-D-Mannosamine Dehydrogenase. Biochem.J. (2014)

Release Date

2014-07-09

Peptides

N-ACYLMANNOSAMINE 1-DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
O

C
D

D
F

N-ACYLMANNOSAMINE 1-DEHYDROGENASE

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