SMTL ID : 8v0j.1

Structure of the complex between Human LIAS and H-protein in the presence of s-adenosyl-l-methionine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.58 Å

Oligo State

hetero-3-3-mer

Ligands

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

SF4.1: 8 residues within 4Å: Chain A: C.137, R.139, C.141, F.143, C.144, V.146, D.181 Ligands: SAM.3 4 PLIP interactions: 4 interactions with chain A, Salt bridges: A:D.181 Metal complexes: A:C.137, A:C.141, A:C.144 SF4.4: 7 residues within 4Å: Chain B: C.137, R.139, C.141, F.143, C.144, D.181 Ligands: SAM.6 5 PLIP interactions: 5 interactions with chain B, Salt bridges: B:D.181, B:E.239 Metal complexes: B:C.137, B:C.141, B:C.144 SF4.7: 7 residues within 4Å: Chain C: C.137, R.139, C.141, F.143, C.144, D.181 Ligands: SAM.9 5 PLIP interactions: 5 interactions with chain C, Salt bridges: C:D.181, C:E.239 Metal complexes: C:C.137, C:C.141, C:C.144

3 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.2: 10 residues within 4Å: Chain A: C.106, C.111, N.113, I.114, C.117, T.129, R.350, S.352, Y.353 Ligands: YVI.10 5 PLIP interactions: 5 interactions with chain A, pi-Cation interactions: A:W.118, A:W.118 Metal complexes: A:C.106, A:C.111, A:C.117 F3S.5: 10 residues within 4Å: Chain B: C.106, C.111, N.113, I.114, C.117, T.129, R.350, S.352, Y.353 Ligands: YVI.11 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.106, B:C.111, B:C.117 F3S.8: 10 residues within 4Å: Chain C: C.106, C.111, N.113, I.114, C.117, T.129, R.350, S.352, Y.353 Ligands: YVI.13 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.106, C:C.111, C:C.117

3 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.3: 19 residues within 4Å: Chain A: V.105, A.109, F.143, C.144, T.178, S.179, V.180, D.181, L.212, P.214, N.237, E.239, M.279, Y.309, M.310, P.312, R.350 Ligands: SF4.1, YVI.10 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.179, A:D.181, A:N.237, A:E.239, A:M.310, A:M.310 pi-Stacking: A:F.143 SAM.6: 21 residues within 4Å: Chain B: V.105, M.131, F.143, T.178, S.179, D.181, L.212, P.214, D.215, H.236, N.237, E.239, M.279, Q.308, Y.309, M.310, P.312, R.350 Chain E: K.107 Ligands: SF4.4, YVI.11 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.181, B:D.215, B:N.237, B:E.239, B:M.310, B:M.310, B:R.350 Water bridges: B:R.249 Salt bridges: B:H.236 pi-Stacking: B:F.143 SAM.9: 20 residues within 4Å: Chain C: V.105, A.109, F.143, T.178, S.179, D.181, L.212, T.213, P.214, H.236, N.237, E.239, M.279, Y.309, M.310, P.312, R.350 Chain F: K.107 Ligands: SF4.7, YVI.13 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.179, C:N.237, C:E.239, C:M.310, C:M.310 Salt bridges: C:H.236 pi-Stacking: C:F.143

3 x YVI: 6-THIOOCTANOIC ACID(Covalent)

YVI.10: 12 residues within 4Å: Chain A: V.105, C.106, A.109, R.110, C.111, P.112, R.350, S.351, S.352 Chain D: K.107 Ligands: F3S.2, SAM.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.350 Hydrogen bonds: A:R.350 YVI.11: 12 residues within 4Å: Chain B: V.105, C.106, A.109, R.110, C.111, P.112, R.350, S.351, S.352 Chain E: K.107 Ligands: F3S.5, SAM.6 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.350 Hydrogen bonds: B:R.350 YVI.13: 11 residues within 4Å: Chain C: V.105, C.106, A.109, R.110, C.111, P.112, R.350, S.352 Chain F: K.107 Ligands: F3S.8, SAM.9 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.105, C:R.350 Hydrogen bonds: C:R.350

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.12: 6 residues within 4Å: Chain E: T.54, E.55, K.96, Q.97, E.157, L.158 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.54, E:E.55, E:Q.97 Salt bridges: E:K.96 PO4.14: 5 residues within 4Å: Chain F: T.54, E.55, K.96, E.157, L.158 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:E.55 Salt bridges: F:K.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Esakova, O.A. et al., Structural basis for the mechanism of the human lipoyl synthase (LIAS) and its complex with the H-protein. To Be Published

Release Date

2025-08-20

Peptides

Lipoyl synthase, mitochondrial: ABC
Glycine cleavage system H protein, mitochondrial: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

D
F

E
D

F
E

Lipoyl synthase, mitochondrial

Glycine cleavage system H protein, mitochondrial

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