SMTL ID : 7uni.1 (1 other biounit)

De novo designed chlorophyll dimer protein with Zn pheophorbide a methyl ester, SP2-ZnPPaM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x OE9: [methyl 9-ethenyl-14-ethyl-3-(3-methoxy-3-oxopropyl)-4,8,13,18-tetramethyl-20-oxophorbine-21-carboxylatato(2-)-kappa~4~N~23~,N~24~,N~25~,N~26~]zinc(Non-covalent)

OE9.1: 14 residues within 4Å: Chain A: N.76, V.132, A.135, H.184, A.187, M.188, A.191, A.240, A.243 Chain B: M.75, A.79 Ligands: EDO.3, PGE.4, OE9.5 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:A.135, A:A.187, A:A.191, A:A.240, A:A.243, B:A.79 Metal complexes: A:H.184 OE9.5: 13 residues within 4Å: Chain A: N.76, A.79 Chain B: V.132, A.135, H.184, A.187, M.188, A.191, A.240, A.243 Ligands: OE9.1, EDO.3, PGE.6 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:A.135, B:A.187, B:A.191, B:A.240, B:A.243, A:A.79 Metal complexes: B:H.184

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 2 residues within 4Å: Chain A: N.194 Chain B: L.195 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.194

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: A.79, A.83 Ligands: OE9.1, OE9.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.79

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 6 residues within 4Å: Chain A: I.128, A.180, W.181, H.184, L.236 Ligands: OE9.1 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:R.72 Hydrogen bonds: A:H.184 PGE.6: 7 residues within 4Å: Chain A: L.20, R.72, M.75 Chain B: I.128, W.181, H.184 Ligands: OE9.5 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:R.125, A:R.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kennedy, M.A. et al., De novo designed chlorophyll dimer protein with Zn pheophorbide a methyl ester, SP2-ZnPPaM. To Be Published

Release Date

2023-04-19

Peptides

SP2-ZnPPaM designed chlorophyll dimer protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

SP2-ZnPPaM designed chlorophyll dimer protein

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