SMTL ID : 2ynm.1

Structure of the ADPxAlF3-Stabilized Transition State of the Nitrogenase-like Dark-Operative Protochlorophyllide Oxidoreductase Complex from Prochlorococcus marinus with Its Substrate Protochlorophyllide a

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-4-2-2-mer

Ligands

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.1: 9 residues within 4Å: Chain A: A.201, K.202, N.203, Y.204, K.205, R.207 Chain D: K.74, F.78, G.110 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:A.201, A:N.203, A:R.207, A:R.207, D:K.74 Water bridges: D:E.71 1PE.20: 9 residues within 4Å: Chain E: A.201, K.202, N.203, Y.204, K.205, R.207 Chain H: K.74, F.78, G.110 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain H Hydrogen bonds: E:A.201, E:N.203, E:R.207, E:R.207, H:K.74 Water bridges: H:E.71

8 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 6 residues within 4Å: Chain A: N.182, S.216, A.217, E.218 Chain B: D.241, R.244 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.182, A:N.182, A:A.217, A:E.218 Salt bridges: A:E.218, A:E.218, B:D.241, B:D.241, B:R.244 EPE.3: 9 residues within 4Å: Chain A: H.74, T.87, I.89, D.90, G.121, G.122 Chain B: K.290, D.291, R.292 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:T.87, A:G.122, B:R.292 Salt bridges: A:D.90, A:D.90, B:D.291, B:R.292 Water bridges: B:R.192, B:D.291 EPE.9: 6 residues within 4Å: Chain A: D.241, R.244 Chain B: N.182, S.216, A.217, E.218 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.182, B:A.217, B:E.218 Salt bridges: B:E.218, B:E.218, A:D.241, A:D.241, A:R.244 EPE.16: 10 residues within 4Å: Chain D: R.180, R.376, V.388, Q.396, D.397, P.399, R.401, S.403, D.417 Chain H: R.401 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain H Hydrogen bonds: D:R.180, D:V.388, D:S.403, D:S.403, H:R.401, H:R.401 Water bridges: D:C.386 Salt bridges: D:R.376, D:D.397, D:D.417, D:D.417 EPE.21: 6 residues within 4Å: Chain E: N.182, S.216, A.217, E.218 Chain F: D.241, R.244 9 PLIP interactions: 6 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:N.182, E:N.182, E:A.217, E:E.218 Salt bridges: E:E.218, E:E.218, F:D.241, F:D.241, F:R.244 EPE.22: 9 residues within 4Å: Chain E: H.74, T.87, I.89, D.90, G.121, G.122 Chain F: K.290, D.291, R.292 8 PLIP interactions: 5 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:R.292, E:G.122 Water bridges: F:R.192, F:D.291 Salt bridges: F:D.291, F:R.292, E:D.90, E:D.90 EPE.28: 6 residues within 4Å: Chain E: D.241, R.244 Chain F: N.182, S.216, A.217, E.218 8 PLIP interactions: 5 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:N.182, F:A.217, F:E.218 Salt bridges: F:E.218, F:E.218, E:D.241, E:D.241, E:R.244 EPE.35: 10 residues within 4Å: Chain D: R.401 Chain H: R.180, R.376, V.388, Q.396, D.397, P.399, R.401, S.403, D.417 11 PLIP interactions: 2 interactions with chain D, 9 interactions with chain H Hydrogen bonds: D:R.401, D:R.401, H:R.180, H:V.388, H:S.403, H:S.403 Water bridges: H:C.386 Salt bridges: H:R.376, H:D.397, H:D.417, H:D.417

4 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.4: 11 residues within 4Å: Chain A: G.43, G.44, K.47, S.48, D.71, K.73, L.158, G.159 Chain B: K.42 Ligands: ADP.5, MG.6 No protein-ligand interaction detected (PLIP) AF3.11: 11 residues within 4Å: Chain A: K.42 Chain B: G.43, G.44, K.47, S.48, D.71, K.73, L.158, G.159 Ligands: MG.10, ADP.12 No protein-ligand interaction detected (PLIP) AF3.23: 11 residues within 4Å: Chain E: G.43, G.44, K.47, S.48, D.71, K.73, L.158, G.159 Chain F: K.42 Ligands: ADP.24, MG.25 No protein-ligand interaction detected (PLIP) AF3.30: 11 residues within 4Å: Chain E: K.42 Chain F: G.43, G.44, K.47, S.48, D.71, K.73, L.158, G.159 Ligands: MG.29, ADP.31 No protein-ligand interaction detected (PLIP)

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

ADP.5: 19 residues within 4Å: Chain A: G.44, I.45, G.46, K.47, S.48, T.49, N.214, R.215, R.238, N.239, V.240, I.243, R.244, R.247 Chain B: K.42, D.183, D.185 Ligands: AF3.4, MG.6 26 PLIP interactions: 8 interactions with chain B, 18 interactions with chain A Hydrogen bonds: B:D.185, B:D.185, B:D.185, A:G.44, A:I.45, A:G.46, A:K.47, A:S.48, A:T.49, A:T.49, A:N.214, A:R.215, A:R.238, A:V.240 Water bridges: B:K.42, B:G.43, B:F.184, A:S.48, A:S.48, A:R.215, A:R.215, A:R.244 Salt bridges: B:K.42, B:K.42, A:K.47, A:R.247 ADP.12: 20 residues within 4Å: Chain A: K.42, D.183, D.185 Chain B: G.44, I.45, G.46, K.47, S.48, T.49, N.214, R.215, F.237, R.238, N.239, V.240, I.243, R.244 Ligands: GOL.8, MG.10, AF3.11 25 PLIP interactions: 17 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:G.44, B:I.45, B:G.46, B:K.47, B:S.48, B:T.49, B:T.49, B:N.214, B:N.214, B:R.215, B:R.215, B:V.240, A:D.183, A:D.185, A:D.185, A:D.185 Water bridges: B:S.48, B:K.73, B:R.244, A:K.42, A:D.183 Salt bridges: B:K.47, B:R.247, A:K.42, A:K.42 ADP.24: 19 residues within 4Å: Chain E: G.44, I.45, G.46, K.47, S.48, T.49, N.214, R.215, R.238, N.239, V.240, I.243, R.244, R.247 Chain F: K.42, D.183, D.185 Ligands: AF3.23, MG.25 25 PLIP interactions: 17 interactions with chain E, 8 interactions with chain F Hydrogen bonds: E:G.44, E:I.45, E:G.46, E:K.47, E:S.48, E:T.49, E:N.214, E:R.215, E:R.238, E:V.240, F:D.183, F:D.185, F:D.185 Water bridges: E:S.48, E:S.48, E:R.215, E:R.215, E:R.244, F:K.42, F:G.43, F:F.184 Salt bridges: E:K.47, E:R.247, F:K.42, F:K.42 ADP.31: 20 residues within 4Å: Chain E: K.42, D.183, D.185 Chain F: G.44, I.45, G.46, K.47, S.48, T.49, N.214, R.215, F.237, R.238, N.239, V.240, I.243, R.244 Ligands: GOL.27, MG.29, AF3.30 22 PLIP interactions: 17 interactions with chain F, 5 interactions with chain E Hydrogen bonds: F:G.44, F:I.45, F:G.46, F:K.47, F:S.48, F:T.49, F:N.214, F:N.214, F:R.215, F:R.215, F:V.240, E:D.185, E:D.185 Water bridges: F:S.48, F:S.48, F:K.73, F:R.244, E:D.183 Salt bridges: F:K.47, F:R.247, E:K.42, E:K.42

4 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 5 residues within 4Å: Chain A: S.48, D.75, D.156 Ligands: AF3.4, ADP.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.48, H2O.1, H2O.1, H2O.1 MG.10: 4 residues within 4Å: Chain B: S.48, D.156 Ligands: AF3.11, ADP.12 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.48, H2O.1, H2O.4, H2O.4 MG.25: 5 residues within 4Å: Chain E: S.48, D.75, D.156 Ligands: AF3.23, ADP.24 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:S.48, H2O.15, H2O.16, H2O.16 MG.29: 4 residues within 4Å: Chain F: S.48, D.156 Ligands: AF3.30, ADP.31 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:S.48, H2O.15, H2O.19, H2O.19

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

SF4.7: 14 residues within 4Å: Chain A: C.129, G.130, G.131, V.162, C.163 Chain B: C.129, G.130, G.131, V.162, C.163 Chain C: V.115, I.116 Chain D: L.99, I.100 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, Metal complexes: A:C.129, A:C.163, B:C.129, B:C.163 SF4.14: 14 residues within 4Å: Chain C: C.25, L.27, T.49, C.50, L.53, S.110, C.111, S.143, G.144 Chain D: P.33, 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.25, C:C.50, C:C.111 SF4.26: 14 residues within 4Å: Chain E: C.129, G.130, G.131, V.162, C.163 Chain F: C.129, G.130, G.131, V.162, C.163 Chain G: V.115, I.116 Chain H: L.99, I.100 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain F, Metal complexes: E:C.129, E:C.163, F:C.129, F:C.163 SF4.33: 14 residues within 4Å: Chain G: C.25, L.27, T.49, C.50, L.53, S.110, C.111, S.143, G.144 Chain H: P.33, Q.34, G.35, D.36, T.96 7 PLIP interactions: 3 interactions with chain G, 4 interactions with chain H, Metal complexes: G:C.25, G:C.50, G:C.111, H:D.36 Salt bridges: H:D.36, H:D.36, H:D.36

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 8 residues within 4Å: Chain A: K.42, G.43, G.44, I.45, D.183, S.186 Chain B: G.44 Ligands: ADP.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.43, A:D.183, A:D.183 Water bridges: A:R.215 GOL.13: 9 residues within 4Å: Chain C: E.22, V.23, F.24, E.301, G.370, M.371, G.372 Chain D: T.37, L.41 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:M.371, C:G.372, D:T.37 Water bridges: C:E.22, C:E.22, C:E.22, D:T.37 GOL.17: 6 residues within 4Å: Chain C: H.52, S.56 Chain D: L.42, I.46, P.392, M.393 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:M.393, C:S.56 Water bridges: D:E.129, D:E.129, C:Q.55 GOL.19: 8 residues within 4Å: Chain A: Q.136, K.139 Chain D: E.93, E.98, Q.101, E.121, L.122, P.123 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:Q.136, A:K.139, D:E.98, D:Q.101 GOL.27: 8 residues within 4Å: Chain E: K.42, G.43, G.44, I.45, D.183, S.186 Chain F: G.44 Ligands: ADP.31 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:G.43, E:D.183, E:D.183 Water bridges: E:R.215 GOL.32: 9 residues within 4Å: Chain G: E.22, V.23, F.24, E.301, G.370, M.371, G.372 Chain H: T.37, L.41 8 PLIP interactions: 3 interactions with chain H, 5 interactions with chain G Hydrogen bonds: H:T.37, H:T.37, G:M.371, G:G.372 Water bridges: H:T.37, G:E.22, G:E.22, G:E.22 GOL.36: 6 residues within 4Å: Chain G: H.52, S.56 Chain H: L.42, I.46, P.392, M.393 5 PLIP interactions: 3 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:M.393, G:S.56 Water bridges: H:E.129, H:E.129, G:Q.55 GOL.38: 8 residues within 4Å: Chain E: Q.136, K.139 Chain H: E.93, E.98, Q.101, E.121, L.122, P.123 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain H Hydrogen bonds: E:Q.136, E:K.139, H:Q.101

2 x PMR: Protochlorophyllide(Non-covalent)

PMR.15: 25 residues within 4Å: Chain C: F.24, T.28, V.31, W.32, L.53, S.56, A.57, F.149, M.371, W.386, I.388, F.392 Chain D: Y.38, L.41, L.42, M.45, I.46, H.394, V.395 Chain H: V.289, D.290, M.424, G.425, L.426, H.429 26 PLIP interactions: 6 interactions with chain D, 9 interactions with chain H, 10 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: D:Y.38, D:L.41, D:M.45, D:I.46, D:V.395, D:V.395, H:D.290, H:L.426, H:L.426, C:F.24, C:T.28, C:V.31, C:W.32, C:L.53, C:A.57, C:F.149, C:W.386, C:F.392, C:F.392 Hydrogen bonds: H:G.425, H:L.426, H:H.429 Water bridges: H:D.290, H:D.290, H:D.290 Metal complexes: H2O.7 PMR.34: 25 residues within 4Å: Chain D: V.289, D.290, M.424, G.425, L.426, H.429 Chain G: F.24, T.28, V.31, W.32, L.53, S.56, A.57, F.149, M.371, W.386, I.388, F.392 Chain H: Y.38, L.41, L.42, M.45, I.46, H.394, V.395 24 PLIP interactions: 10 interactions with chain G, 6 interactions with chain H, 7 interactions with chain D, 1 Ligand-Water interactions, Hydrophobic interactions: G:F.24, G:T.28, G:V.31, G:W.32, G:L.53, G:A.57, G:F.149, G:W.386, G:F.392, G:F.392, H:Y.38, H:L.41, H:M.45, H:I.46, H:V.395, H:V.395, D:D.290, D:L.426, D:L.426 Hydrogen bonds: D:G.425, D:L.426 Water bridges: D:D.290, D:D.290 Metal complexes: H2O.22

2 x K: POTASSIUM ION(Non-covalent)

K.18: 3 residues within 4Å: Chain C: R.48 Chain D: E.2, K.128 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.2, D:E.2, H2O.12 K.37: 3 residues within 4Å: Chain G: R.48 Chain H: E.2, K.128 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.2, H:E.2, H2O.27

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moser, J. et al., Structure of Adp-Aluminium Fluoride-Stabilized Protochlorophyllide Oxidoreductase Complex. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-01-30

Peptides

LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE IRON-SULFUR ATP-BINDING PROTEIN: ABEF
LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT N: CG
LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT B: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
A

F
B

C
C

G
C

D
D

H
D

LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE IRON-SULFUR ATP-BINDING PROTEIN

LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT N

LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT B