SMTL ID : 7unj.1

De novo designed chlorophyll dimer protein with Zn pheophorbide a methyl ester matching geometry of purple bacterial special pair, SP1-ZnPPaM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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: 18 residues within 4Å: Chain A: M.64, L.67, L.71, L.75, W.119, L.120, H.123, M.126, L.127, W.130 Chain B: I.8, Y.11, Q.12, L.15, M.64, L.67, L.71 Ligands: OE9.4 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:L.67, A:L.71, A:L.75, A:W.119, A:L.120, A:L.127, A:W.130, B:Y.11, B:L.15, B:L.67, B:L.67 Metal complexes: A:H.123 Hydrogen bonds: B:Q.12 OE9.4: 17 residues within 4Å: Chain A: I.8, Y.11, Q.12, L.15, M.64, L.67, L.71 Chain B: M.64, L.67, L.71, L.75, W.119, H.123, M.126, L.127, W.130 Ligands: OE9.1 14 PLIP interactions: 7 interactions with chain A, 7 interactions with chain B, Hydrophobic interactions: A:Y.11, A:L.15, A:L.67, A:L.67, A:L.71, A:L.71, B:L.67, B:L.71, B:L.75, B:W.119, B:L.127, B:W.130 Hydrogen bonds: A:Q.12 Metal complexes: B:H.123

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 1 residues within 4Å: Chain A: R.40 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.36, A:R.40

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

EDO.3: 4 residues within 4Å: Chain A: R.22, V.77, R.78, E.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.22, A:E.81 EDO.5: 3 residues within 4Å: Chain B: M.64, S.116, W.119 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.119 EDO.6: 4 residues within 4Å: Chain B: S.170, S.171, K.172, E.173 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.171, B:K.172

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ennist, N.M. et al., De novo design of proteins housing excitonically coupled chlorophyll special pairs. Nat.Chem.Biol. (2024)

Release Date

2023-04-19

Peptides

SP1-ZnPPaM designed chlorophyll dimer protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

SP1-ZnPPaM designed chlorophyll dimer protein