SMTL ID : 6tjr.1

Structure of HdrA-like subunit from Hyphomicrobium denitrificans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

homo-dimer

Ligands

2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 12 residues within 4Å: Chain A: L.162, C.163, S.166, R.167, C.176, S.177, K.178, I.179, C.180, C.181, D.206, R.208 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.163, A:C.176, A:C.180, A:C.181 SF4.6: 12 residues within 4Å: Chain B: L.162, C.163, S.166, R.167, C.176, S.177, K.178, I.179, C.180, C.181, D.206, R.208 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.163, B:C.176, B:C.180, B:C.181

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.2: 36 residues within 4Å: Chain A: V.7, G.8, G.9, G.10, P.11, A.12, V.30, E.31, K.32, R.33, G.38, A.39, P.40, Y.45, L.48, V.49, T.79, T.108, T.109, G.110, F.111, H.113, T.133, T.134, E.137, I.179, V.183, N.273, D.275, I.279, G.314, S.315, E.320, T.321, I.322, S.325 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:T.134, A:E.137, A:V.183 Hydrogen bonds: A:G.9, A:A.12, A:K.32, A:K.32, A:R.33, A:G.38, A:A.39, A:Y.45, A:Y.45, A:V.49, A:V.49, A:F.111, A:N.273, A:D.275, A:S.315, A:S.315, A:E.320, A:I.322, A:S.325 Water bridges: A:G.10, A:G.13, A:R.33, A:F.111, A:Y.213, A:A.316, A:D.323 pi-Stacking: A:Y.45 FAD.7: 36 residues within 4Å: Chain B: V.7, G.8, G.9, G.10, P.11, A.12, V.30, E.31, K.32, R.33, G.38, A.39, P.40, Y.45, L.48, V.49, T.108, T.109, G.110, F.111, H.113, T.133, T.134, E.137, I.179, V.183, M.270, N.273, D.275, I.279, G.314, S.315, E.320, T.321, I.322, S.325 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:T.134, B:V.183 Hydrogen bonds: B:G.9, B:A.12, B:K.32, B:K.32, B:R.33, B:G.38, B:A.39, B:Y.45, B:V.49, B:V.49, B:F.111, B:N.273, B:D.275, B:D.275, B:S.315, B:S.315, B:E.320, B:I.322, B:S.325 Water bridges: B:G.10, B:G.13, B:R.33, B:F.111, B:Y.213, B:A.316, B:D.323 pi-Stacking: B:Y.45

5 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3: 5 residues within 4Å: Chain A: W.54, N.56, I.140, S.141, G.143 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.56 Water bridges: A:N.56 MES.4: 5 residues within 4Å: Chain A: F.42, S.43, H.113, T.134, Q.138 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.138 Water bridges: A:T.134, A:T.134 Salt bridges: A:H.113 MES.5: 3 residues within 4Å: Chain A: R.53 Chain B: D.297, G.300 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Salt bridges: A:R.53 Hydrogen bonds: B:G.300 Water bridges: B:D.297, B:D.297, B:L.301 MES.8: 4 residues within 4Å: Chain A: K.296, D.297, G.300 Chain B: R.53 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:R.53 Hydrogen bonds: A:G.300 Water bridges: A:K.296, A:L.301 MES.9: 5 residues within 4Å: Chain B: F.42, S.43, H.113, T.134, Q.138 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.43, B:T.134, B:Q.138 Salt bridges: B:H.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ernst, C. et al., Structural and spectroscopic characterization of a HdrA-like subunit from Hyphomicrobium denitrificans. Febs J. (2021)

Release Date

2020-08-19

Peptides

Fumarate reductase/succinate dehydrogenase flavoprotein domain protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Fumarate reductase/succinate dehydrogenase flavoprotein domain protein