SMTL ID : 4wwj.1 (1 other biounit)

UndA, an oxygen-activating, non-heme iron dependent desaturase/decarboxylase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x FE: FE (III) ION(Non-covalent)

FE.1: 5 residues within 4Å: Chain A: E.103, H.106, H.196 Ligands: GOL.2, SO4.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.103, A:H.106, A:H.196, H2O.11 FE.10: 5 residues within 4Å: Chain B: E.103, H.106, H.196 Ligands: GOL.11, SO4.17 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.103, B:H.106, B:H.196, H2O.23

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 11 residues within 4Å: Chain A: V.67, F.70, E.103, H.106, E.161, T.164, W.192, H.196 Ligands: FE.1, GOL.4, SO4.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.164 GOL.3: 7 residues within 4Å: Chain A: Y.43, Y.59, G.63, L.136, M.238, F.241 Ligands: GOL.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.43, A:Y.43 Water bridges: A:G.62, A:G.63 GOL.4: 11 residues within 4Å: Chain A: G.63, V.66, V.67, W.110, I.160, T.164, W.167, W.192, M.238 Ligands: GOL.2, GOL.3 No protein-ligand interaction detected (PLIP) GOL.5: 2 residues within 4Å: Chain A: R.98 Chain B: R.101 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.101, A:R.98, A:R.98 Water bridges: B:R.101 GOL.11: 11 residues within 4Å: Chain B: V.67, F.70, E.103, H.106, E.161, T.164, W.192, H.196 Ligands: FE.10, GOL.13, SO4.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.164, B:T.164 GOL.12: 7 residues within 4Å: Chain B: Y.43, Y.59, G.63, L.136, M.238, F.241 Ligands: GOL.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.43, B:Y.43 Water bridges: B:G.62, B:G.63 GOL.13: 11 residues within 4Å: Chain B: G.63, V.66, V.67, W.110, I.160, T.164, W.167, W.192, M.238 Ligands: GOL.11, GOL.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.164 GOL.14: 2 residues within 4Å: Chain A: R.101 Chain B: R.98 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.101, B:R.98, B:R.98 Water bridges: A:R.101

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

SO4.6: 2 residues within 4Å: Chain A: R.94, R.98 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:N.105, A:R.94 Salt bridges: A:R.94, A:R.98 SO4.7: 3 residues within 4Å: Chain A: R.101, N.105, Y.109 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.109 Water bridges: A:R.101, A:V.102, A:N.105 Salt bridges: A:R.101 SO4.8: 10 residues within 4Å: Chain A: F.70, W.95, N.99, V.102, E.103, E.161, D.200, H.203 Ligands: FE.1, GOL.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.99, A:E.161 Salt bridges: A:H.203 SO4.9: 6 residues within 4Å: Chain A: H.86, P.87, G.88, E.89, D.90, M.91 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.88, A:D.90, A:M.91 SO4.15: 2 residues within 4Å: Chain B: R.94, R.98 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:R.94, A:N.105 Salt bridges: B:R.94, B:R.98 SO4.16: 3 residues within 4Å: Chain B: R.101, N.105, Y.109 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.101, B:V.102, B:N.105 Salt bridges: B:R.101 SO4.17: 10 residues within 4Å: Chain B: F.70, W.95, N.99, V.102, E.103, E.161, D.200, H.203 Ligands: FE.10, GOL.11 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.99, B:E.103, B:E.161 Water bridges: B:H.106 Salt bridges: B:H.203 SO4.18: 6 residues within 4Å: Chain B: H.86, P.87, G.88, E.89, D.90, M.91 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.88, B:D.90, B:D.90, B:M.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rui, Z. et al., Microbial biosynthesis of medium-chain 1-alkenes by a nonheme iron oxidase. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-12-24

Peptides

TENA/THI-4 family protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

TENA/THI-4 family protein

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