SMTL ID : 3fwy.1

Crystal structure of the L protein of Rhodobacter sphaeroides light-independent protochlorophyllide reductase (BchL) with MgADP bound: a homologue of the nitrogenase Fe protein

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: S.62, D.85, D.89 Ligands: ADP.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.62, H2O.1, H2O.1, H2O.2, H2O.2 MG.3: 4 residues within 4Å: Chain B: S.62, D.85, D.89 Ligands: ADP.5 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.62, H2O.10, H2O.10, H2O.10, H2O.10

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 18 residues within 4Å: Chain A: K.56, G.58, I.59, G.60, K.61, S.62, T.63, K.87, N.228, R.229, M.251, P.252, D.253, L.254, I.257, R.258, R.261 Ligands: MG.1 25 PLIP interactions: 24 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.58, A:I.59, A:G.60, A:K.61, A:S.62, A:T.63, A:T.63, A:N.228, A:R.229, A:R.229, A:P.252, A:L.254 Water bridges: A:K.61, A:S.62, A:T.63, A:D.85, A:K.87, A:K.87, A:K.87, A:K.87, B:D.199 Salt bridges: A:K.61, A:K.87, A:K.87 pi-Cation interactions: A:R.229 ADP.5: 18 residues within 4Å: Chain B: K.56, G.58, I.59, G.60, K.61, S.62, T.63, K.87, N.228, R.229, M.251, P.252, D.253, L.254, I.257, R.258, R.261 Ligands: MG.3 28 PLIP interactions: 27 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.58, B:I.59, B:G.60, B:K.61, B:S.62, B:T.63, B:T.63, B:N.228, B:R.229, B:R.229, B:P.252, B:D.253, B:L.254, B:R.258 Water bridges: B:K.61, B:S.62, B:S.62, B:D.85, B:D.85, B:K.87, B:K.87, B:K.87, B:D.170, A:D.199 Salt bridges: B:K.61, B:K.87, B:K.87 pi-Cation interactions: B:R.229

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

SF4.4: 11 residues within 4Å: Chain A: C.143, G.144, G.145, C.177, G.178 Chain B: C.143, G.144, G.145, C.177, G.178, F.180 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, Metal complexes: B:C.143, B:C.177, A:C.143, A:C.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sarma, R. et al., Crystal Structure of the L Protein of Rhodobacter sphaeroides Light-Independent Protochlorophyllide Reductase with MgADP Bound: A Homologue of the Nitrogenase Fe Protein. Biochemistry (2008)

Release Date

2009-03-24

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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