SMTL ID : 6jku.1

Crystal structure of N-acetylglucosamine-6-phosphate deacetylase from Pasteurella Multocida

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: Q.76, E.145, H.157, H.209, H.230 Ligands: PO4.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.145, A:H.209, A:H.230 ZN.16: 6 residues within 4Å: Chain B: Q.76, E.145, H.157, H.209, H.230 Ligands: PO4.17 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.145, B:H.209, B:H.230 ZN.28: 6 residues within 4Å: Chain C: Q.76, E.145, H.157, H.209, H.230 Ligands: PO4.29 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.145, C:H.209, C:H.230 ZN.37: 6 residues within 4Å: Chain D: Q.76, E.145, H.157, H.209, H.230 Ligands: PO4.38 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.145, D:H.209, D:H.230

15 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 11 residues within 4Å: Chain A: N.78, E.145, V.156, H.157, H.209, H.230, D.287, L.320, G.321, G.322 Ligands: ZN.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.287, A:L.320, A:G.322 Water bridges: A:Q.76 Salt bridges: A:H.157, A:H.209, A:H.230 PO4.3: 5 residues within 4Å: Chain A: K.154, H.157, R.158, E.159, E.160 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.159, A:E.160 Water bridges: A:K.154, A:V.156 Salt bridges: A:K.154 PO4.4: 3 residues within 4Å: Chain A: D.43, K.44, K.136 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.43 Water bridges: A:K.136, A:K.136 Salt bridges: A:K.44, A:K.136 PO4.5: 4 residues within 4Å: Chain A: N.233, A.234 Chain B: S.240, R.242 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:N.233, A:A.234 Water bridges: A:K.153, A:M.235, B:R.242, B:R.242, B:R.242, B:R.242, B:R.242 Salt bridges: B:R.242 PO4.6: 3 residues within 4Å: Chain A: R.242 Chain B: N.233, A.234 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:R.242, A:R.242 Salt bridges: A:R.242 Hydrogen bonds: B:N.233, B:A.234 PO4.17: 10 residues within 4Å: Chain B: N.78, E.145, V.156, H.157, H.209, H.230, D.287, G.321, G.322 Ligands: ZN.16 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.287, B:L.320, B:G.322 Water bridges: B:Q.76 Salt bridges: B:H.157, B:H.209, B:H.230 PO4.18: 5 residues within 4Å: Chain B: K.304, D.315, N.317, T.319 Ligands: EDO.24 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.315, B:D.315, B:N.317, B:T.319 Water bridges: B:K.304, B:K.304 Salt bridges: B:K.154, B:K.304 PO4.19: 3 residues within 4Å: Chain B: D.43, K.44, K.136 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.43 Salt bridges: B:K.44, B:K.136 PO4.29: 10 residues within 4Å: Chain C: N.78, E.145, V.156, H.157, H.209, H.230, D.287, G.321, G.322 Ligands: ZN.28 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:N.78, C:E.145, C:D.287, C:G.322 Water bridges: C:Q.76, C:V.156, C:V.156, C:L.320, C:G.322 Salt bridges: C:H.157, C:H.209, C:H.230 PO4.30: 4 residues within 4Å: Chain C: N.233, A.234 Chain D: S.240 Ligands: EDO.35 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:N.233, C:A.234 Water bridges: C:K.153, C:K.153, C:H.232, C:M.235, D:S.240 PO4.31: 5 residues within 4Å: Chain C: S.240, R.242 Chain D: N.233, A.234 Ligands: EDO.45 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:N.233, D:A.234 Water bridges: C:R.242, C:R.242 Salt bridges: C:R.242 PO4.38: 10 residues within 4Å: Chain D: N.78, E.145, V.156, H.157, H.209, H.230, D.287, G.321, G.322 Ligands: ZN.37 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:N.78, D:D.287, D:G.322 Water bridges: D:Q.76, D:V.156, D:L.320, D:G.322 Salt bridges: D:H.157, D:H.209, D:H.230 PO4.39: 6 residues within 4Å: Chain D: G.155, K.304, D.315, N.317, T.319 Ligands: PO4.40 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.155, D:D.315, D:N.317 Water bridges: D:K.304 Salt bridges: D:K.304 PO4.40: 6 residues within 4Å: Chain D: K.154, H.157, R.158, E.159, K.304 Ligands: PO4.39 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:H.157, D:E.159, D:E.159 Water bridges: D:E.160, D:E.160, D:K.304 Salt bridges: D:K.154, D:R.158, D:K.304 PO4.41: 3 residues within 4Å: Chain D: D.43, K.44, I.371 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:K.44

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

EDO.7: 6 residues within 4Å: Chain A: N.23, A.24, Y.34, G.35 Chain C: N.379, D.380 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: D.118, R.163 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: A.292, G.293, A.324, I.325, T.326, E.329 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: Y.214, M.244 Chain B: D.267, Y.268, G.269 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: K.275, G.339, I.340, P.341, E.344 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain A: D.280, K.281 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain A: K.332, Q.336, N.379, D.380, F.381 Chain C: G.35 Ligands: EDO.32 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain B: N.23, A.24, Y.34, G.35 Chain D: N.379, D.380 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: T.213, Y.214, D.215, R.242 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain B: D.280, K.281 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: A.292, G.293, A.324, T.326, E.329 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain B: K.154, H.157, R.158, E.159, E.160, K.304 Ligands: PO4.18 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain B: F.172, D.175, N.176 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain A: N.379, D.380 Chain C: N.23, A.24, Y.34, G.35 Ligands: EDO.13 Ligand excluded by PLIP EDO.33: 2 residues within 4Å: Chain C: T.213, D.215 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain C: A.291, A.292, G.293, A.324, I.325, E.329 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain C: E.152, K.153, K.154, G.155, A.234 Ligands: PO4.30 Ligand excluded by PLIP EDO.42: 6 residues within 4Å: Chain B: N.379, D.380 Chain D: N.23, A.24, Y.34, G.35 Ligand excluded by PLIP EDO.43: 5 residues within 4Å: Chain D: T.213, Y.214, D.215, R.242, A.243 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain D: Y.351, D.360, S.365, E.367, K.370 Ligand excluded by PLIP EDO.45: 6 residues within 4Å: Chain D: E.152, K.153, K.154, G.155, A.234 Ligands: PO4.31 Ligand excluded by PLIP EDO.46: 5 residues within 4Å: Chain D: G.303, K.304, T.305, D.315, S.316 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 7 residues within 4Å: Chain A: Q.64, G.65, N.66 Chain C: Q.64, G.65, N.66, N.379 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:N.66, C:N.66, C:N.379 Water bridges: A:N.379, C:Q.64, C:Q.64 GOL.26: 6 residues within 4Å: Chain B: Q.64, N.66, N.379 Chain D: Q.64, G.65, N.66 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Water bridges: D:G.65, D:N.66, D:N.379, B:N.66 Hydrogen bonds: B:N.379

4 x NA: SODIUM ION(Non-functional Binders)

NA.15: 3 residues within 4Å: Chain A: A.177, I.180, G.202 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.202 NA.27: 3 residues within 4Å: Chain B: A.177, I.180, G.202 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.180 NA.36: 3 residues within 4Å: Chain C: A.177, I.180, G.202 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.202 NA.47: 3 residues within 4Å: Chain D: A.177, I.180, G.202 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manjunath, L. et al., Quaternary variations in the structural assembly of N-acetylglucosamine-6-phosphate deacetylase from Pasteurella multocida. Proteins (2020)

Release Date

2020-03-04

Peptides

N-acetylglucosamine-6-phosphate deacetylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

N-acetylglucosamine-6-phosphate deacetylase