SMTL ID : 8vqj.1

CryoEM structure of DPOR under turnover

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.82 Å

Oligo State

hetero-2-2-2-mer

Ligands

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

SF4.1: 10 residues within 4Å: Chain A: C.29, L.31, C.54, L.57, C.115, S.147 Chain B: P.33, Q.34, G.35, D.36 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B, Metal complexes: A:C.29, A:C.54, A:C.115, B:D.36 Salt bridges: B:D.36, B:D.36, B:D.36 SF4.6: 11 residues within 4Å: Chain C: C.29, L.31, C.54, L.57, C.115, P.116, G.146 Chain D: P.33, Q.34, G.35, D.36 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C, Salt bridges: D:D.36, D:D.36, D:D.36 Metal complexes: D:D.36, C:C.29, C:C.54, C:C.115 SF4.8: 12 residues within 4Å: Chain E: Q.40, C.147, G.148, G.149, C.181, F.184 Chain F: C.147, G.148, G.149, C.181, G.183, F.184 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E, Metal complexes: F:C.147, F:C.181 pi-Cation interactions: E:F.184

2 x PMR: Protochlorophyllide(Non-covalent)

PMR.2: 17 residues within 4Å: Chain A: F.28, T.32, I.35, L.57, S.60, A.61, L.375, W.390, I.392, E.393, F.396 Chain B: Y.38, L.41, M.45, I.46 Chain D: V.273, D.274 12 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A, 1 interactions with chain D, Hydrophobic interactions: B:Y.38, B:L.41, B:M.45, B:I.46, A:F.28, A:F.28, A:I.35, A:L.57, A:I.392, A:F.396, A:F.396 Hydrogen bonds: D:D.274 PMR.3: 13 residues within 4Å: Chain B: D.274, L.410, L.414 Chain C: W.36, S.60, A.61, A.62, W.390, I.392, F.396 Chain D: L.41, M.45, V.379 8 PLIP interactions: 3 interactions with chain D, 4 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: D:L.41, D:M.45, D:V.379, C:W.36, C:I.392, C:F.396, C:F.396, B:L.414

2 x CU: COPPER (II) ION(Non-covalent)

CU.4: 4 residues within 4Å: Chain B: H.404, M.408 Chain D: M.408 Ligands: CU.5 No protein-ligand interaction detected (PLIP) CU.5: 4 residues within 4Å: Chain B: H.404, M.408 Chain D: M.408 Ligands: CU.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.404

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 2 residues within 4Å: Chain E: T.67, L.266 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain F: K.65, D.89, K.91 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kashyap, R. et al., Cryo-EM captures the coordination of asymmetric electron transfer through a di-copper site in DPOR. Nat Commun (2025)

Release Date

2025-04-30

Peptides

Light-independent protochlorophyllide reductase subunit N: AC
Light-independent protochlorophyllide reductase subunit B: BD
Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
F

Light-independent protochlorophyllide reductase subunit N

Light-independent protochlorophyllide reductase subunit B

Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein

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