SMTL ID : 2yi1.1

Crystal structure of N-Acetylmannosamine kinase in complex with N- acetyl mannosamine 6-phosphate and ADP.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x BMX: 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-mannopyranose(Non-covalent)

BMX.1: 22 residues within 4Å: Chain A: G.38, G.39, G.98, G.99, R.100, S.111, T.112, L.114, I.115, N.139, D.140, G.166, T.167, G.168, I.169, G.170, E.189, H.192, E.211 Ligands: BM3.2, MG.3, ADP.13 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.115 Hydrogen bonds: A:G.39, A:G.99, A:R.100, A:R.100, A:T.112, A:N.139, A:D.140, A:G.166, A:T.167, A:G.168, A:E.189, A:E.189 Water bridges: A:D.140, A:G.170 Salt bridges: A:H.192 BMX.15: 22 residues within 4Å: Chain B: G.38, G.39, G.98, G.99, R.100, S.111, T.112, L.114, I.115, N.139, D.140, G.166, T.167, G.168, I.169, G.170, E.189, H.192, E.211 Ligands: BM3.16, MG.17, ADP.27 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.115 Hydrogen bonds: B:G.39, B:G.99, B:R.100, B:R.100, B:T.112, B:N.139, B:N.139, B:D.140, B:G.166, B:T.167, B:T.167, B:G.168, B:E.189, B:E.189 Water bridges: B:T.112, B:G.170 Salt bridges: B:H.192

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

BM3.2: 15 residues within 4Å: Chain A: G.98, G.99, R.100, S.111, T.112, L.114, I.115, N.139, D.140, I.169, G.170, E.189, H.192, E.211 Ligands: BMX.1 10 PLIP interactions: 10 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 Salt bridges: A:H.192 BM3.16: 15 residues within 4Å: Chain B: G.98, G.99, R.100, S.111, T.112, L.114, I.115, N.139, D.140, I.169, G.170, E.189, H.192, E.211 Ligands: BMX.15 12 PLIP interactions: 12 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 Salt bridges: B:H.192

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.36 Ligands: BMX.1, ADP.13 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.36, H2O.1, H2O.1, H2O.6 MG.17: 3 residues within 4Å: Chain B: D.36 Ligands: BMX.15, ADP.27 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.36, H2O.6, H2O.6, H2O.11

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 1 residues within 4Å: Chain A: Q.116 No protein-ligand interaction detected (PLIP) CA.5: 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.3 CA.18: 1 residues within 4Å: Chain B: Q.116 No protein-ligand interaction detected (PLIP) 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.9

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

2PE.6: 5 residues within 4Å: Chain A: V.54, K.55, K.56, Y.57, E.82 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.55 Water bridges: A:K.56, A:K.56 2PE.20: 5 residues within 4Å: Chain B: V.54, K.55, K.56, Y.57, 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)

PG4.7: 5 residues within 4Å: Chain A: G.39, T.40, F.60, N.61, K.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.63 Water bridges: A:K.63 PG4.21: 5 residues within 4Å: Chain B: G.39, T.40, F.60, N.61, K.63 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.63 Water bridges: B:K.63

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

EDO.8: 1 residues within 4Å: Chain A: L.71 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.74 EDO.9: 5 residues within 4Å: Chain A: R.104, G.182, S.183, F.185 Ligands: ACT.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.104 EDO.10: 4 residues within 4Å: Chain A: Q.315, D.316, V.317, D.318 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.315, A:D.318 EDO.11: 3 residues within 4Å: Chain A: N.41, T.58, F.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.41 Water bridges: A:F.60 EDO.22: 1 residues within 4Å: Chain B: L.71 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.74 EDO.23: 5 residues within 4Å: Chain B: R.104, G.182, S.183, F.185 Ligands: ACT.26 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.104 EDO.24: 4 residues within 4Å: Chain B: Q.315, D.316, V.317, D.318 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.315, B:D.318 EDO.25: 3 residues within 4Å: Chain B: N.41, T.58, F.60 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.41 Water bridges: B:F.60

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

ACT.12: 6 residues within 4Å: Chain A: I.180, H.181, G.182 Chain B: E.158, H.175 Ligands: EDO.9 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:H.175 Hydrogen bonds: A:H.181, A:G.182 ACT.26: 6 residues within 4Å: Chain A: E.158, H.175 Chain B: I.180, H.181, G.182 Ligands: EDO.23 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.181, B:G.182 Salt bridges: A:H.175

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

ADP.13: 12 residues within 4Å: Chain A: G.38, G.39, T.40, N.41, R.43, G.166, T.167, G.216, L.248, V.293 Ligands: BMX.1, MG.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:G.39, A:T.40, A:T.40, A:N.41, A:N.41, A:N.41, A:T.167 Water bridges: A:G.38, A:N.41, A:D.140, A:G.216, A:L.248, A:V.293, A:V.293 Salt bridges: A:R.43 ADP.27: 12 residues within 4Å: Chain B: G.38, G.39, T.40, N.41, R.43, G.166, T.167, G.216, L.248, V.293 Ligands: BMX.15, MG.17 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:G.39, B:T.40, B:T.40, B:T.40, B:N.41, B:N.41, B:N.41, B:T.167, B:T.167 Water bridges: B:G.38, B:N.41, B:G.216, B:L.248, B:V.293, B:V.293 Salt bridges: B:R.43

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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