SMTL ID : 5l2r.1

Crystal structure of fumarate hydratase from Leishmania major

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

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

LMR.1: 13 residues within 4Å: Chain A: Q.170, D.171, R.209, G.251, G.252, R.457, T.503, T.504, R.507, K.527 Chain B: H.370, A.372 Ligands: SF4.8 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:D.171 Hydrogen bonds: A:Q.170, A:G.251, A:G.252, A:T.503, A:T.504 Water bridges: A:G.487 Salt bridges: A:R.209, A:R.457, A:R.507, A:K.527, B:H.370 LMR.2: 7 residues within 4Å: Chain A: N.255, K.256, Y.258, A.286, T.504, R.507 Chain B: Q.261 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.255, A:N.255, A:K.256, B:Q.261 Water bridges: A:T.504, A:T.504, A:T.504 Salt bridges: A:K.256, A:K.256 LMR.9: 13 residues within 4Å: Chain A: H.370, A.372 Chain B: Q.170, D.171, R.209, G.251, G.252, R.457, T.503, T.504, R.507, K.527 Ligands: SF4.19 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:D.171 Hydrogen bonds: B:Q.170, B:D.171, B:G.251, B:G.252, B:T.504 Water bridges: B:G.487 Salt bridges: B:R.209, B:R.457, B:R.507, B:K.527, A:H.370 LMR.10: 6 residues within 4Å: Chain A: Q.261 Chain B: N.255, K.256, Y.258, A.286, R.507 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.255, B:K.256, B:Y.258, B:Y.258 Water bridges: B:N.255, B:N.255, B:T.504 Salt bridges: B:K.256, B:K.256

4 x MLA: MALONIC ACID(Non-covalent)

MLA.3: 8 residues within 4Å: Chain A: I.176, L.178, Q.231, D.233, K.307, K.310 Chain B: E.303 Ligands: GOL.6 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.176 Hydrogen bonds: A:Q.231, B:E.303 Salt bridges: A:K.307, A:K.310 MLA.4: 12 residues within 4Å: Chain A: P.76, H.77, H.78, F.83, K.180, E.243, F.244, Y.316, L.389, A.390, H.391 Ligands: GOL.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.389 Hydrogen bonds: A:E.243, A:E.243 Salt bridges: A:H.78, A:K.180, A:H.391 MLA.11: 7 residues within 4Å: Chain A: E.303 Chain B: I.176, L.178, Q.231, D.233, K.307, K.310 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.176 Hydrogen bonds: B:Q.231, A:E.303 Salt bridges: B:K.310 MLA.12: 11 residues within 4Å: Chain B: P.76, H.77, H.78, F.83, K.180, E.243, F.244, Y.316, L.389, A.390, H.391 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.389 Hydrogen bonds: B:H.77, B:E.243, B:E.243 Salt bridges: B:H.78, B:K.180, B:H.391

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: P.73, P.76, H.78, K.180, Y.316, Y.317 Ligands: MLA.4, GOL.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.180, A:K.180, A:Y.316 GOL.6: 9 residues within 4Å: Chain A: Q.231, L.232, D.233, K.307 Chain B: E.303, M.304, K.307 Ligands: MLA.3, PEG.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.232 Water bridges: A:D.233 GOL.7: 7 residues within 4Å: Chain A: F.71, L.235, K.307, Y.316, Y.317 Ligands: GOL.5, GOL.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.307, A:Y.316, A:Y.316 GOL.13: 7 residues within 4Å: Chain B: P.73, P.76, H.78, K.180, Y.316, Y.317 Ligands: GOL.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.76, B:K.180, B:Y.316 GOL.14: 6 residues within 4Å: Chain A: A.236 Chain B: E.192, L.232, D.233, L.234 Ligands: GOL.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.232, B:L.234, B:L.234 Water bridges: B:D.233 GOL.15: 8 residues within 4Å: Chain A: R.101 Chain B: K.105, V.106, P.108, W.186, T.187, G.188 Ligands: GOL.17 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.101, B:V.106 GOL.16: 8 residues within 4Å: Chain B: F.71, K.180, L.235, K.307, Y.316, Y.317 Ligands: GOL.13, PEG.18 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.180, B:K.180, B:K.307, B:K.307, B:Y.316, B:Y.317 GOL.17: 8 residues within 4Å: Chain B: K.91, Y.92, V.93, E.94, K.105, V.106, N.107 Ligands: GOL.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.91, B:V.93

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

SF4.8: 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.1 4 PLIP interactions: 4 interactions with chain A, Salt bridges: A:D.171 Metal complexes: A:C.169, A:C.288, A:C.382 SF4.19: 13 residues within 4Å: Chain B: 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.9 4 PLIP interactions: 4 interactions with chain B, Salt bridges: B:D.171 Metal complexes: B:C.169, B:C.288, B:C.382

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.18: 9 residues within 4Å: Chain A: A.230, Q.231, L.232 Chain B: I.70, F.71, M.304, K.307 Ligands: GOL.6, GOL.16 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.232, B:K.307, B:K.307 Water bridges: A:A.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feliciano, P.R. et al., Crystal structure of an Fe-S cluster-containing fumarate hydratase enzyme from Leishmania major reveals a unique protein fold. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-08-17

Peptides

Fumarate hydratase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Fumarate hydratase

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