SMTL ID : 9buo.1

CryoEM structure of DPOR in the presence of ADP-AlF3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.68 Å

Oligo State

hetero-4-2-2-mer

Ligands

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

SF4.1: 10 residues within 4Å: Chain A: Y.150, V.152, C.181, G.182, G.183, F.184 Chain B: C.147, C.181, G.182, G.183 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, Metal complexes: A:C.181, A:G.182, B:C.181 SF4.2: 13 residues within 4Å: Chain C: C.29, L.31, T.53, C.54, L.57, C.115, P.116, G.148 Chain D: P.33, Q.34, G.35, D.36, C.95 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D, Metal complexes: C:C.29, C:C.54, C:C.115, D:D.36 Salt bridges: D:D.36, D:D.36, D:D.36 SF4.5: 10 residues within 4Å: Chain E: C.29, L.31, C.54, C.115, P.116, G.148 Chain F: P.33, Q.34, D.36, C.95 8 PLIP interactions: 3 interactions with chain E, 5 interactions with chain F, Metal complexes: E:C.29, E:C.54, E:C.115, F:D.36 Salt bridges: F:D.36, F:D.36, F:D.36 pi-Cation interactions: F:Y.38 SF4.8: 14 residues within 4Å: Chain G: G.146, C.147, G.148, V.152, C.181, G.182, G.183 Chain H: G.146, C.147, G.148, G.149, C.181, G.182, G.183 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain G, Metal complexes: H:C.181, G:C.147

2 x PMR: Protochlorophyllide(Non-covalent)

PMR.3: 14 residues within 4Å: Chain C: F.28, T.32, I.35, S.60, A.61, L.375, W.390, I.392, E.393 Chain D: Y.38, L.41, M.45 Chain F: V.273, D.274 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D, Hydrophobic interactions: C:F.28, C:F.28, C:I.35, C:A.61, C:I.392, D:Y.38, D:L.41 PMR.6: 16 residues within 4Å: Chain D: D.274, Y.277 Chain E: F.28, I.35, S.60, A.61, G.63, W.390, I.392, E.393, F.396 Chain F: L.41, L.42, M.45, I.46, V.379 11 PLIP interactions: 6 interactions with chain E, 5 interactions with chain F, Hydrophobic interactions: E:F.28, E:I.35, E:A.61, E:W.390, E:I.392, E:F.396, F:L.41, F:L.41, F:M.45, F:I.46, F:V.379

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

CU.4: 5 residues within 4Å: Chain D: H.404, M.408 Chain F: H.404, M.408 Ligands: CU.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.404 CU.7: 5 residues within 4Å: Chain D: H.404, M.408 Chain F: H.404, M.408 Ligands: CU.4 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 iron-sulfur ATP-binding protein: ABGH
Light-independent protochlorophyllide reductase subunit N: CE
Light-independent protochlorophyllide reductase subunit B: DF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

G
E

H
F

C
A

E
C

D
B

F
D

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

Light-independent protochlorophyllide reductase subunit N

Light-independent protochlorophyllide reductase subunit B

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