SMTL ID : 6m0a.2 (1 other biounit)

The heme-bound structure of the chloroplast protein At3g03890

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 15 residues within 4Å: Chain A: A.99, V.100, S.101, L.103, A.104, V.105, H.106, T.107, W.162, F.168 Chain B: V.184, A.185, T.186, L.189 Ligands: AZI.2 16 PLIP interactions: 3 interactions with chain B, 12 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: B:V.184, B:A.185, B:L.189, A:A.104, A:W.162, A:W.162, A:F.168, A:F.168 Hydrogen bonds: A:S.101, A:V.105, A:T.107 Water bridges: A:H.106 Salt bridges: A:H.106, A:H.106 pi-Stacking: A:F.168 Metal complexes: H2O.5 HEM.3: 13 residues within 4Å: Chain A: V.184, A.185, T.186, L.189 Chain B: V.100, S.101, L.103, A.104, V.105, H.106, W.162, F.168 Ligands: AZI.4 14 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: B:A.104, B:W.162, B:F.168, B:F.168, A:V.184, A:A.185, A:L.189 Hydrogen bonds: B:S.101, B:L.103, B:V.105 Salt bridges: B:H.106, B:H.106 pi-Stacking: B:F.168 Metal complexes: H2O.5

2 x AZI: AZIDE ION(Non-covalent)

AZI.2: 3 residues within 4Å: Chain A: D.167, F.168 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) AZI.4: 2 residues within 4Å: Chain B: D.167 Ligands: HEM.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.167

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J. et al., The Arabidopsis locus AT3G03890 encodes a dimeric beta-barrel protein implicated in heme degradation. Biochem.J. (2020)

Release Date

2020-12-16

Peptides

AT3G03890 protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

AT3G03890 protein

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