SMTL ID : 8aw5.1

Cryo-EM structure of heme A synthase trimer from Aquifex aeolicus

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 23 residues within 4Å: Chain A: L.149, Q.190, I.191, G.194, V.197, R.198, H.213, I.214, A.217, L.220, M.243, Q.246, I.247, G.250, V.251, V.254, F.258, L.263, H.266, I.267, F.271, I.273 Ligands: POV.3 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:Q.190, A:I.191, A:V.197, A:I.214, A:L.220, A:Q.246, A:I.247, A:I.247, A:V.251, A:F.258, A:L.263, A:I.273 Salt bridges: A:R.198, A:R.198 Metal complexes: A:H.266 HEM.5: 23 residues within 4Å: Chain B: L.149, Q.190, I.191, G.194, V.197, R.198, H.213, I.214, A.217, L.220, M.243, Q.246, I.247, G.250, V.251, V.254, F.258, L.263, H.266, I.267, F.271, I.273 Ligands: POV.7 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:Q.190, B:I.191, B:V.197, B:I.214, B:L.220, B:Q.246, B:I.247, B:I.247, B:V.251, B:F.258, B:L.263, B:I.273 Salt bridges: B:R.198, B:R.198 Metal complexes: B:H.266 HEM.9: 23 residues within 4Å: Chain C: L.149, Q.190, I.191, G.194, V.197, R.198, H.213, I.214, A.217, L.220, M.243, Q.246, I.247, G.250, V.251, V.254, F.258, L.263, H.266, I.267, F.271, I.273 Ligands: POV.10 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:Q.190, C:I.191, C:V.197, C:I.214, C:L.220, C:Q.246, C:I.247, C:I.247, C:V.251, C:F.258, C:L.263, C:I.273 Salt bridges: C:R.198, C:R.198 Metal complexes: C:H.266

9 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.2: 20 residues within 4Å: Chain A: S.105, F.106, K.109, F.113, I.116, V.153, T.158, Y.184, M.188, L.192, I.195, Y.289 Chain B: I.222, L.225, F.226, M.228, F.229, K.230, F.232 Ligands: POV.7 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.113, A:F.113, A:F.113, A:F.113, A:I.116, A:V.153, A:T.158, A:Y.184, A:L.192, A:I.195, B:I.222, B:L.225, B:F.229, B:F.229, B:F.229 Salt bridges: A:K.109 POV.3: 18 residues within 4Å: Chain A: Y.210, Y.211, I.214, I.222, L.225, V.251, V.254 Chain C: V.143, A.147, I.150, L.151, L.192, F.196, V.200, A.202, Y.205 Ligands: HEM.1, POV.12 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:I.222, A:L.225, A:V.251, A:V.251, A:V.254, C:I.150, C:L.151, C:L.192, C:F.196, C:F.196, C:V.200 Hydrogen bonds: A:Y.210 POV.4: 8 residues within 4Å: Chain A: Y.23, E.171, K.234, Y.235, I.238, I.269, F.272, W.276 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.23, A:I.238, A:I.269, A:F.272, A:F.272, A:F.272, A:W.276 Hydrogen bonds: A:Y.235 Salt bridges: A:K.167, A:K.234 POV.6: 20 residues within 4Å: Chain B: S.105, F.106, K.109, F.113, I.116, V.153, T.158, Y.184, M.188, L.192, I.195, Y.289 Chain C: I.222, L.225, F.226, M.228, F.229, K.230, F.232 Ligands: POV.10 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:F.113, B:F.113, B:I.116, B:V.153, B:T.158, B:Y.184, B:L.192, B:I.195, C:I.222, C:L.225, C:F.229, C:F.229, C:F.229 Salt bridges: B:K.109 POV.7: 18 residues within 4Å: Chain A: V.143, A.147, I.150, L.151, L.192, F.196, V.200, A.202, Y.205 Chain B: Y.210, Y.211, I.214, I.222, L.225, V.251, V.254 Ligands: POV.2, HEM.5 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:I.150, A:I.150, A:L.151, A:F.196, A:F.196, A:V.200, B:I.222, B:L.225, B:V.251, B:V.251, B:V.254 Hydrogen bonds: B:Y.210 POV.8: 8 residues within 4Å: Chain B: Y.23, E.171, K.234, Y.235, I.238, I.269, F.272, W.276 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.23, B:I.238, B:I.269, B:F.272, B:F.272, B:F.272, B:W.276 Hydrogen bonds: B:Y.235 Salt bridges: B:K.167, B:K.234 POV.10: 19 residues within 4Å: Chain B: L.120, V.143, A.147, I.150, L.151, L.192, F.196, V.200, A.202, Y.205 Chain C: Y.210, Y.211, I.214, I.222, L.225, V.251, V.254 Ligands: POV.6, HEM.9 15 PLIP interactions: 9 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:L.120, B:I.150, B:I.150, B:L.151, B:L.192, B:L.192, B:F.196, B:F.196, B:V.200, C:I.222, C:L.225, C:V.251, C:V.251, C:V.254 Hydrogen bonds: C:Y.210 POV.11: 8 residues within 4Å: Chain C: Y.23, E.171, K.234, Y.235, I.238, I.269, F.272, W.276 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Y.23, C:I.238, C:I.269, C:F.272, C:F.272, C:F.272, C:W.276 Hydrogen bonds: C:Y.235 Salt bridges: C:K.167, C:K.234 POV.12: 20 residues within 4Å: Chain A: I.222, L.225, F.226, M.228, F.229, K.230, F.232 Chain C: S.105, F.106, K.109, F.113, I.116, V.153, T.158, Y.184, M.188, L.192, I.195, Y.289 Ligands: POV.3 14 PLIP interactions: 5 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: A:I.222, A:L.225, A:F.229, A:F.229, A:F.229, C:F.113, C:F.113, C:I.116, C:V.153, C:T.158, C:Y.184, C:L.192, C:I.195 Salt bridges: C:K.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hui, Z. et al., Cryo-EM structure of heme A synthase trimer from Aquifex aeolicus. To Be Published

Release Date

2023-09-06

Peptides

Heme O oxygenase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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Heme O oxygenase