SMTL ID : 2yhw.1

High-resolution crystal structures of N-Acetylmannosamine kinase: Insights about substrate specificity, activity and inhibitor modelling.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

homo-dimer

Ligands

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

BM3.1: 15 residues within 4Å: Chain A: G.98, G.99, R.100, S.111, T.112, L.114, I.115, N.139, D.140, G.168, I.169, G.170, E.189, H.192, E.211 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.115 Hydrogen bonds: A:G.99, A:R.100, A:R.100, A:T.112, A:N.139, A:N.139, A:E.189, A:E.189 Water bridges: A:G.168, A:G.171 Salt bridges: A:H.192 BM3.13: 15 residues within 4Å: Chain B: G.98, G.99, R.100, S.111, T.112, L.114, I.115, N.139, D.140, G.168, I.169, G.170, E.189, H.192, E.211 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.115 Hydrogen bonds: B:G.99, B:R.100, B:R.100, B:T.112, B:N.139, B:N.139, B:E.189, B:E.189 Water bridges: B:T.112, B:G.168, B:G.171 Salt bridges: B:H.192

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.192, C.202, C.204, C.209 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.192, A:C.202, A:C.204, A:C.209 ZN.14: 4 residues within 4Å: Chain B: H.192, C.202, C.204, C.209 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.192, B:C.202, B:C.204, B:C.209

2 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.3: 4 residues within 4Å: Chain A: V.54, K.55, K.56, E.82 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.55 Water bridges: A:K.56, A:K.56 2PE.15: 4 residues within 4Å: Chain B: V.54, K.55, K.56, E.82 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.55 Water bridges: B:K.56, B:K.56

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 4 residues within 4Å: Chain A: Q.59, L.71, Q.74, M.75 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.74 EDO.5: 3 residues within 4Å: Chain A: A.80, A.81, V.84 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.77 EDO.6: 4 residues within 4Å: Chain A: N.41, T.58, Q.59, F.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.41 Water bridges: A:F.60 EDO.9: 2 residues within 4Å: Chain A: D.316, D.318 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.316, A:V.317 EDO.16: 4 residues within 4Å: Chain B: Q.59, L.71, Q.74, M.75 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.74 EDO.17: 3 residues within 4Å: Chain B: A.80, A.81, V.84 1 PLIP interactions: 1 interactions with chain B Water bridges: B:V.77 EDO.18: 4 residues within 4Å: Chain B: N.41, T.58, Q.59, F.60 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.41 Water bridges: B:F.60 EDO.21: 2 residues within 4Å: Chain B: D.316, D.318 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.316, B:V.317

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 5 residues within 4Å: Chain A: N.139, N.142, G.171, A.187, A.188 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.171, A:A.188, H2O.5 CA.19: 5 residues within 4Å: Chain B: N.139, N.142, G.171, A.187, A.188 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.171, B:A.188, H2O.14

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.8: 2 residues within 4Å: Chain A: K.63 Ligands: PGE.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.63 PGE.10: 6 residues within 4Å: Chain A: G.39, T.40, F.60, N.61, K.63 Ligands: PGE.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.63 Water bridges: A:L.114 PGE.20: 2 residues within 4Å: Chain B: K.63 Ligands: PGE.22 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.63 PGE.22: 6 residues within 4Å: Chain B: G.39, T.40, F.60, N.61, K.63 Ligands: PGE.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.63 Water bridges: B:L.114

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.11: 6 residues within 4Å: Chain A: L.179, I.180, H.181, G.182 Chain B: E.158, H.175 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.181, A:H.181, A:G.182 Water bridges: A:L.179 Salt bridges: B:H.175 ACT.23: 6 residues within 4Å: Chain A: E.158, H.175 Chain B: L.179, I.180, H.181, G.182 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.181, B:G.182 Water bridges: B:L.179, A:H.175 Salt bridges: A:H.175

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 1 residues within 4Å: Chain A: Q.116 Ligand excluded by PLIP CL.24: 1 residues within 4Å: Chain B: Q.116 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martinez, J. et al., Crystal Structures of N-Acetylmannosamine Kinase Provide Insights Into Enzyme Specificity and Inhibition. J.Biol.Chem. (2012)

Release Date

2012-02-29

Peptides

BIFUNCTIONAL UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE/N-ACETYLMANNOSAMINE KINASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

BIFUNCTIONAL UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE/N-ACETYLMANNOSAMINE KINASE