SMTL ID : 3men.2 (1 other biounit)

Crystal structure of acetylpolyamine aminohydrolase from Burkholderia pseudomallei, iodide soak

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.213, M.214, H.215, D.302 Ligands: SO4.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.213, A:D.213, A:H.215, A:D.302 ZN.12: 5 residues within 4Å: Chain B: D.213, M.214, H.215, D.302 Ligands: SO4.13 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.213, B:D.213, B:H.215, B:D.302

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 10 residues within 4Å: Chain A: H.177, H.178, G.186, F.187, D.213, H.215, D.302, G.339, Y.341 Ligands: ZN.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.186 Salt bridges: A:H.177, A:H.178, A:H.215 SO4.13: 11 residues within 4Å: Chain B: P.175, H.177, H.178, G.186, F.187, D.213, H.215, D.302, G.339, Y.341 Ligands: ZN.12 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.186, B:Y.341 Salt bridges: B:H.177, B:H.178, B:H.215 SO4.15: 2 residues within 4Å: Chain B: R.45, M.46 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.45, B:M.46

2 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain A: D.211, D.213, H.215, S.234, I.235 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.211, A:D.211, A:D.213, A:H.215 K.14: 5 residues within 4Å: Chain B: D.211, D.213, H.215, S.234, I.235 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.211, B:D.211, B:H.215, B:S.234, B:I.235

17 x IOD: IODIDE ION(Non-functional Binders)

IOD.4: 3 residues within 4Å: Chain A: D.238, M.267, P.268 Ligand excluded by PLIP IOD.5: 4 residues within 4Å: Chain A: H.34, G.140, E.141, H.142 Ligand excluded by PLIP IOD.6: 3 residues within 4Å: Chain A: F.90, T.93, E.97 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: S.40, R.41 Chain B: N.112 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: L.287, L.331 Ligand excluded by PLIP IOD.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: S.40, S.136 Ligand excluded by PLIP IOD.11: 1 residues within 4Å: Chain A: Q.221 Ligand excluded by PLIP IOD.16: 3 residues within 4Å: Chain B: D.238, M.267, P.268 Ligand excluded by PLIP IOD.17: 4 residues within 4Å: Chain A: N.112 Chain B: S.40, R.41, Y.243 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain B: T.93, E.97 Ligand excluded by PLIP IOD.19: 2 residues within 4Å: Chain B: L.287, R.288 Ligand excluded by PLIP IOD.20: 4 residues within 4Å: Chain B: H.34, G.140, E.141, H.142 Ligand excluded by PLIP IOD.21: 1 residues within 4Å: Chain B: Q.221 Ligand excluded by PLIP IOD.22: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.23: 3 residues within 4Å: Chain B: Y.38, S.40, S.136 Ligand excluded by PLIP IOD.24: 5 residues within 4Å: Chain B: R.162, A.199, L.200, R.203, H.204 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., SAD phasing using iodide ions in a high-throughput structural genomics environment. J Struct Funct Genomics (2011)

Release Date

2010-04-21

Peptides

Acetylpolyamine aminohydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Acetylpolyamine aminohydrolase

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