SMTL ID : 9efu.1

CryoEM structure of BchN-BchB electron acceptor component protein of DPOR with Pchlide

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.92 Å

Oligo State

hetero-2-2-mer

Ligands

2 x SF4: IRON/SULFUR CLUSTER(Covalent)

SF4.1: 12 residues within 4Å: Chain A: C.29, L.31, T.53, C.54, S.114, C.115, P.116, G.148 Chain B: P.33, G.35, D.36, T.96 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 SF4.3: 12 residues within 4Å: Chain C: C.29, L.31, C.54, L.57, S.114, C.115, P.116, G.148 Chain D: Q.34, G.35, D.36, T.96 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

2 x PMR: Protochlorophyllide(Non-covalent)

PMR.2: 19 residues within 4Å: Chain A: F.28, T.32, I.35, S.60, A.61, L.375, W.390, I.392, E.393, F.396 Chain B: Y.38, L.41, L.42, M.45, I.46, V.379 Chain D: V.273, D.274, L.410 15 PLIP interactions: 8 interactions with chain B, 7 interactions with chain A, Hydrophobic interactions: B:Y.38, B:L.41, B:L.41, B:L.42, B:M.45, B:I.46, B:V.379, B:V.379, A:I.35, A:A.61, A:L.375, A:I.392, A:I.392, A:F.396, A:F.396 PMR.4: 18 residues within 4Å: Chain B: V.273, D.274 Chain C: F.28, T.32, I.35, L.57, S.60, A.61, L.375, W.390, I.392, F.396 Chain D: Y.38, L.41, L.42, M.45, I.46, V.379 20 PLIP interactions: 7 interactions with chain D, 12 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: D:Y.38, D:L.41, D:L.42, D:M.45, D:I.46, D:V.379, D:V.379, C:F.28, C:I.35, C:L.57, C:A.61, C:L.375, C:W.390, C:W.390, C:I.392, C:F.396, C:F.396, C:F.396 pi-Stacking: C:F.396 Hydrogen bonds: B:D.274

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

CU.5: 5 residues within 4Å: Chain B: H.404, M.408 Chain D: H.404, M.408 Ligands: CU.6 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.404 CU.6: 5 residues within 4Å: Chain B: H.404, M.408 Chain D: H.404, M.408 Ligands: CU.5 No protein-ligand interaction detected (PLIP)

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

2025-05-07

Peptides

Light-independent protochlorophyllide reductase subunit N: AC
Light-independent protochlorophyllide reductase subunit B: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Light-independent protochlorophyllide reductase subunit N

Light-independent protochlorophyllide reductase subunit B

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