SMTL ID : 2yhy.1

Structure of N-Acetylmannosamine kinase in complex with N- acetylmannosamine and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 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:E.189, A:E.189 Water bridges: A:G.39, A:G.168, A:G.170 Salt bridges: A:H.192 BM3.15: 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 14 PLIP interactions: 14 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:G.39, B:T.112, B:G.168, B:G.170 Salt bridges: B:H.192

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 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.4 CA.16: 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.11

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.17: 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

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

PG4.4: 3 residues within 4Å: Chain A: D.316, V.317, D.318 4 PLIP interactions: 4 interactions with chain A Water bridges: A:S.286, A:D.316, A:D.316, A:D.318 PG4.18: 3 residues within 4Å: Chain B: D.316, V.317, D.318 4 PLIP interactions: 4 interactions with chain B Water bridges: B:S.286, B:D.316, B:D.316, B:D.318

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

EDO.5: 3 residues within 4Å: Chain A: 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.8: 1 residues within 4Å: Chain A: L.71 No protein-ligand interaction detected (PLIP) EDO.12: 5 residues within 4Å: Chain A: L.179, I.180, H.181, G.182 Chain B: H.175 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.181, A:H.181, A:G.182, B:H.175 EDO.19: 3 residues within 4Å: Chain B: 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.22: 1 residues within 4Å: Chain B: L.71 No protein-ligand interaction detected (PLIP) EDO.26: 5 residues within 4Å: Chain A: H.175 Chain B: L.179, I.180, H.181, G.182 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.181, B:G.182, A:H.175

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

PGE.6: 3 residues within 4Å: Chain A: R.124, V.135, W.136 No protein-ligand interaction detected (PLIP) PGE.9: 6 residues within 4Å: Chain A: G.39, T.40, F.60, N.61, K.63 Ligands: PGE.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.63 PGE.10: 2 residues within 4Å: Chain A: K.63 Ligands: PGE.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.63 PGE.20: 3 residues within 4Å: Chain B: R.124, V.135, W.136 No protein-ligand interaction detected (PLIP) PGE.23: 6 residues within 4Å: Chain B: G.39, T.40, F.60, N.61, K.63 Ligands: PGE.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.63 PGE.24: 2 residues within 4Å: Chain B: K.63 Ligands: PGE.23 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.63

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 2 residues within 4Å: Chain A: D.36 Ligands: ADP.11 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.36, H2O.1, H2O.1, H2O.1, H2O.1 MG.21: 2 residues within 4Å: Chain B: D.36 Ligands: ADP.25 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.36, H2O.8, H2O.8, H2O.8, H2O.8

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.11: 13 residues within 4Å: Chain A: G.38, G.39, T.40, N.41, R.43, G.166, T.167, G.216, M.217, Q.220, L.248, V.293 Ligands: MG.7 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:G.39, A:T.40, A:N.41, A:N.41, A:N.41, A:T.167, A:T.167, A:Q.220 Water bridges: A:G.38, A:G.38, A:R.43, A:R.43, A:G.168, A:A.247 Salt bridges: A:R.43 ADP.25: 13 residues within 4Å: Chain B: G.38, G.39, T.40, N.41, R.43, G.166, T.167, G.216, M.217, Q.220, L.248, V.293 Ligands: MG.21 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:G.39, B:T.40, B:N.41, B:N.41, B:N.41, B:T.167, B:T.167, B:Q.220 Water bridges: B:G.38, B:G.38, B:R.43, B:R.43, B:G.168, B:A.247 Salt bridges: B:R.43

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

CL.13: 1 residues within 4Å: Chain A: Q.116 Ligand excluded by PLIP CL.27: 1 residues within 4Å: Chain B: Q.116 Ligand excluded by PLIP

2 x ZN: ZINC ION(Non-covalent)

ZN.14: 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.28: 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

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

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