SMTL ID : 3qxs.1

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with ANP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: N.30, H.169, N.171 Ligands: EDO.15 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: N.152, L.154, D.155, L.184, H.188 Ligands: EDO.14 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: F.94, Y.95, R.96, Y.97, D.111 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: C.144, E.151, N.152 Chain B: L.179, Y.212 Ligands: EDO.14 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: F.19, V.51, D.133, L.239 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: L.210, I.213, N.217, I.224, V.225, I.226, Q.229 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: V.63, N.64, D.65, R.96, Y.97, H.98 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: R.40, L.41, Q.44, D.79 Ligand excluded by PLIP EDO.12: 1 residues within 4Å: Chain A: S.207 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: H.22, M.23, K.161, K.163, S.242 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: E.150, N.152, D.155 Ligands: EDO.4, EDO.7 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain B: N.30, H.169, N.171 Ligands: EDO.1 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain B: N.152, L.154, D.155, L.184, H.188 Ligands: EDO.28 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain B: F.94, Y.95, R.96, Y.97, D.111 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: L.179, Y.212 Chain B: C.144, E.151, N.152 Ligands: EDO.28 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain B: F.19, V.51, D.133, L.239 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain B: L.210, I.213, N.217, I.224, V.225, I.226, Q.229 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain B: V.63, N.64, D.65, R.96, Y.97, H.98 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain B: R.40, L.41, Q.44, D.79 Ligand excluded by PLIP EDO.26: 1 residues within 4Å: Chain B: S.207 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain B: H.22, M.23, K.161, K.163, S.242 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain B: E.150, N.152, D.155 Ligands: EDO.18, EDO.21 Ligand excluded by PLIP

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.2: 14 residues within 4Å: Chain A: T.31, N.32, A.33, G.34, K.35, T.36, T.37, K.57, D.72, E.138, N.197, K.199, Q.228 Ligands: MG.3 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:N.32, A:N.32, A:G.34, A:K.35, A:K.35, A:T.36, A:T.36, A:T.37, A:T.37, A:K.57, A:N.197, A:N.197, A:K.199, A:Q.228 Water bridges: A:T.31, A:K.35, A:G.200, A:G.200, A:G.200, A:G.200 pi-Cation interactions: A:K.199 ANP.16: 14 residues within 4Å: Chain B: T.31, N.32, A.33, G.34, K.35, T.36, T.37, K.57, D.72, E.138, N.197, K.199, Q.228 Ligands: MG.17 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:T.31, B:N.32, B:N.32, B:G.34, B:K.35, B:K.35, B:T.36, B:T.37, B:T.37, B:K.57, B:N.197, B:N.197, B:K.199, B:Q.228 Water bridges: B:T.31, B:K.35, B:T.36, B:T.36, B:G.200, B:G.200, B:G.200, B:G.200 pi-Cation interactions: B:K.199

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: T.36, K.57, D.72, E.138 Ligands: ANP.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.36, A:D.72, A:E.138, H2O.9 MG.17: 5 residues within 4Å: Chain B: T.36, K.57, D.72, E.138 Ligands: ANP.16 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.36, B:D.72, B:E.138, H2O.21

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.5: 10 residues within 4Å: Chain A: F.25, S.27, A.28, K.35, G.139, A.140, G.141, G.142, L.143, M.153 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.27, A:A.28, A:K.35, A:A.140, A:G.142 Water bridges: A:G.141, A:G.141 NO3.19: 10 residues within 4Å: Chain B: F.25, S.27, A.28, K.35, G.139, A.140, G.141, G.142, L.143, M.153 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.27, B:A.28, B:K.35, B:A.140, B:G.142 Water bridges: B:G.141, B:G.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Porebski, P.J. et al., Structural characterization of Helicobacter pylori dethiobiotin synthetase reveals differences between family members. Febs J. (2012)

Release Date

2011-03-30

Peptides

Dethiobiotin synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Dethiobiotin synthetase

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