SMTL ID : 6uqm.1

Crystal structure of R173A variant of cytosolic fumarate hydratase from Leishmania major in a complex with S-malate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: C.169, Q.170, D.171, G.250, G.252, S.253, A.287, C.288, C.382, A.384, P.502, K.527 Ligands: LMR.2 4 PLIP interactions: 4 interactions with chain A, Salt bridges: A:D.171 Metal complexes: A:C.169, A:C.288, A:C.382 SF4.6: 14 residues within 4Å: Chain B: C.169, Q.170, D.171, G.250, G.252, S.253, A.287, C.288, C.382, S.383, A.384, P.502, K.527 Ligands: LMR.7 4 PLIP interactions: 4 interactions with chain B, Salt bridges: B:D.171 Metal complexes: B:C.169, B:C.288, B:C.382

2 x LMR: (2S)-2-hydroxybutanedioic acid(Non-covalent)

LMR.2: 12 residues within 4Å: Chain A: Q.170, D.171, G.251, G.252, R.457, P.502, T.503, T.504, R.507, K.527 Chain B: A.372 Ligands: SF4.1 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.170, A:D.171, A:G.251, A:G.252, A:T.504 Water bridges: A:R.457 Salt bridges: A:R.457, A:R.507, A:K.527 Hydrophobic interactions: B:A.372 LMR.7: 12 residues within 4Å: Chain A: A.372 Chain B: Q.170, D.171, G.251, G.252, R.457, P.502, T.503, T.504, R.507, K.527 Ligands: SF4.6 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.170, B:D.171, B:G.251, B:G.252, B:T.504 Water bridges: B:R.457, B:R.457, B:R.457 Salt bridges: B:R.457, B:R.507, B:K.527 Hydrophobic interactions: A:A.372

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: L.259, Y.260, Q.261 Chain B: Y.258 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.261 GOL.4: 8 residues within 4Å: Chain A: Y.210, S.211, N.223, R.457, E.575 Chain B: H.370, G.371, A.372 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.223, A:R.457, A:R.457, A:E.575, A:E.575, B:H.370 Water bridges: A:D.171, A:Y.210, A:T.213, A:L.572 GOL.5: 5 residues within 4Å: Chain A: N.255, K.256, Y.258, R.507 Chain B: Q.261 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.255, A:K.256 Water bridges: A:K.256, A:Y.258, A:T.282, A:T.504, A:T.504 GOL.8: 6 residues within 4Å: Chain B: K.91, Y.92, V.93, E.94, K.105, N.107 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.91, B:N.107, B:N.107 Water bridges: B:V.106 GOL.9: 8 residues within 4Å: Chain A: G.371 Chain B: T.213, C.222, N.223, I.459, L.572, M.574, E.575 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.213, B:N.223, B:N.223, B:L.572, B:E.575 Water bridges: B:E.221 GOL.10: 7 residues within 4Å: Chain A: I.70, F.71, M.304 Chain B: E.192, A.230, Q.231, L.232 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:L.232 Water bridges: B:A.230, B:D.233, A:K.307, A:K.307

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feliciano, P.R. et al., Structural and Biochemical Investigations of the [4Fe-4S] Cluster-Containing Fumarate Hydratase fromLeishmania major. Biochemistry (2019)

Release Date

2019-12-04

Peptides

Fumarate hydratase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Fumarate hydratase 2

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