SMTL ID : 3vdi.1

Structure of the FMO protein from Pelodictyon phaeum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-trimer

Ligands

21 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 28 residues within 4Å: Chain A: V.104, V.106, F.109, H.111, F.113, M.150, V.152, L.154, D.158, L.159, T.162, W.163, F.166, F.177, I.181, F.184, W.185, I.204, V.206, G.220, S.222, W.224 Chain B: S.127, A.129, V.130 Ligands: BCL.2, BCL.6, BCL.7 19 PLIP interactions: 1 interactions with chain B, 18 interactions with chain A, Hydrophobic interactions: B:V.130, A:V.104, A:F.109, A:F.113, A:V.152, A:L.159, A:F.166, A:F.166, A:F.166, A:F.166, A:F.177, A:I.181, A:F.184, A:I.204, A:V.206, A:W.224, A:W.224, A:W.224 Metal complexes: A:H.111 BCL.2: 30 residues within 4Å: Chain A: L.42, P.43, L.44, C.49, I.71, S.73, V.75, N.80, K.81, L.82, V.104, V.106, F.113, F.115, M.150, F.184, W.185, I.187 Chain B: Y.125, V.130, V.134, P.137, V.138, Y.139, Q.141 Ligands: BCL.1, BCL.3, BCL.4, BCL.6, BCL.7 21 PLIP interactions: 14 interactions with chain A, 6 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: A:L.42, A:P.43, A:L.44, A:V.75, A:N.80, A:L.82, A:L.82, A:V.104, A:V.106, A:F.113, A:F.115, A:F.115, A:I.187, A:I.187, B:Y.139, B:Y.139 Hydrogen bonds: B:V.138, B:Y.139, B:Q.141 Water bridges: B:Y.125 Metal complexes: H2O.1 BCL.3: 26 residues within 4Å: Chain A: A.12, S.14, Y.16, A.34, V.38, P.39, A.40, A.41, L.42, F.186, A.190, F.259, S.261, I.266, V.268, H.299, V.302, G.303, N.306, F.308, C.354 Ligands: BCL.2, BCL.4, BCL.5, BCL.6, BCL.7 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:A.12, A:A.34, A:V.38, A:F.186, A:A.190, A:F.259, A:I.266, A:V.268, A:V.268, A:V.302, A:V.302, A:N.306, A:F.308, A:F.308, A:F.308 Hydrogen bonds: A:A.41, A:L.42 Metal complexes: A:H.299 BCL.4: 28 residues within 4Å: Chain A: Y.16, I.18, K.31, G.32, C.49, I.51, G.257, G.258, F.259, V.270, I.288, L.289, H.291, P.292, P.295, L.296, H.299, L.314, Y.346, W.349, V.350, C.354, F.361 Ligands: BCL.2, BCL.3, BCL.5, BCL.6, BCL.7 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:Y.16, A:Y.16, A:I.18, A:F.259, A:V.270, A:L.289, A:P.292, A:P.295, A:P.295, A:L.296, A:H.299, A:W.349, A:V.350 Metal complexes: A:H.291 BCL.5: 25 residues within 4Å: Chain A: I.30, I.51, I.53, A.55, V.65, F.67, I.71, I.88, D.235, R.239, E.242, L.243, F.244, P.245, L.249, I.255, L.274, P.275, G.276, L.289, P.292 Ligands: BCL.3, BCL.4, BCL.6, BCL.7 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:I.51, A:I.53, A:A.55, A:I.71, A:I.88, A:L.243, A:L.243, A:F.244, A:L.249, A:I.255, A:I.255, A:L.274, A:P.275, A:L.289 Water bridges: A:D.235 Salt bridges: A:R.239 Metal complexes: A:L.243 BCL.6: 31 residues within 4Å: Chain A: I.53, A.55, F.67, L.82, V.84, V.86, I.88, R.96, I.97, A.98, G.117, V.119, Q.144, H.146, I.148, W.185, F.226, H.228, S.236, W.240, L.243, A.253, S.254, I.255, L.274 Ligands: BCL.1, BCL.2, BCL.3, BCL.4, BCL.5, BCL.7 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:I.53, A:A.55, A:F.67, A:F.67, A:L.82, A:V.84, A:A.98, A:V.119, A:W.185, A:F.226, A:F.226, A:W.240, A:L.243, A:A.253, A:I.255, A:L.274 Hydrogen bonds: A:R.96 Metal complexes: A:H.146 BCL.7: 24 residues within 4Å: Chain A: A.41, L.42, I.71, L.82, F.186, I.187, P.189, A.190, A.193, I.194, Q.199, I.294, P.295, H.298, H.299, M.301, V.302 Chain B: Y.139 Ligands: BCL.1, BCL.2, BCL.3, BCL.4, BCL.5, BCL.6 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:L.42, A:I.71, A:F.186, A:F.186, A:I.187, A:P.189, A:A.190, A:I.194, A:P.295, A:P.295, A:M.301 Hydrogen bonds: A:Q.199 pi-Stacking: A:H.298 Metal complexes: A:H.298 BCL.12: 28 residues within 4Å: Chain B: V.104, V.106, F.109, H.111, F.113, M.150, V.152, L.154, D.158, L.159, T.162, W.163, F.166, F.177, I.181, F.184, W.185, I.204, V.206, G.220, S.222, W.224 Chain C: S.127, A.129, V.130 Ligands: BCL.13, BCL.17, BCL.18 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:V.104, B:F.109, B:F.113, B:V.152, B:L.159, B:F.166, B:F.166, B:F.166, B:F.166, B:F.177, B:I.181, B:F.184, B:I.204, B:V.206, B:W.224, B:W.224, B:W.224, C:V.130 Metal complexes: B:H.111 BCL.13: 30 residues within 4Å: Chain B: L.42, P.43, L.44, C.49, I.71, S.73, V.75, N.80, K.81, L.82, V.104, V.106, F.113, F.115, M.150, F.184, W.185, I.187 Chain C: Y.125, V.130, V.134, P.137, V.138, Y.139, Q.141 Ligands: BCL.12, BCL.14, BCL.15, BCL.17, BCL.18 21 PLIP interactions: 14 interactions with chain B, 6 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: B:L.42, B:P.43, B:L.44, B:V.75, B:N.80, B:L.82, B:L.82, B:V.104, B:V.106, B:F.113, B:F.115, B:F.115, B:I.187, B:I.187, C:Y.139, C:Y.139 Hydrogen bonds: C:V.138, C:Y.139, C:Q.141 Water bridges: C:Y.125 Metal complexes: H2O.8 BCL.14: 26 residues within 4Å: Chain B: A.12, S.14, Y.16, A.34, V.38, P.39, A.40, A.41, L.42, F.186, A.190, F.259, S.261, I.266, V.268, H.299, V.302, G.303, N.306, F.308, C.354 Ligands: BCL.13, BCL.15, BCL.16, BCL.17, BCL.18 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:A.12, B:A.34, B:V.38, B:F.186, B:A.190, B:F.259, B:I.266, B:V.268, B:V.268, B:V.302, B:V.302, B:N.306, B:F.308, B:F.308, B:F.308 Hydrogen bonds: B:A.41, B:L.42 Metal complexes: B:H.299 BCL.15: 28 residues within 4Å: Chain B: Y.16, I.18, K.31, G.32, C.49, I.51, G.257, G.258, F.259, V.270, I.288, L.289, H.291, P.292, P.295, L.296, H.299, L.314, Y.346, W.349, V.350, C.354, F.361 Ligands: BCL.13, BCL.14, BCL.16, BCL.17, BCL.18 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:Y.16, B:Y.16, B:I.18, B:F.259, B:V.270, B:L.289, B:P.292, B:P.295, B:P.295, B:L.296, B:H.299, B:W.349, B:V.350 Metal complexes: B:H.291 BCL.16: 25 residues within 4Å: Chain B: I.30, I.51, I.53, A.55, V.65, F.67, I.71, I.88, D.235, R.239, E.242, L.243, F.244, P.245, L.249, I.255, L.274, P.275, G.276, L.289, P.292 Ligands: BCL.14, BCL.15, BCL.17, BCL.18 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:I.51, B:I.53, B:A.55, B:I.71, B:I.88, B:L.243, B:L.243, B:F.244, B:L.249, B:I.255, B:I.255, B:L.274, B:P.275, B:L.289 Water bridges: B:D.235 Salt bridges: B:R.239 Metal complexes: B:L.243 BCL.17: 31 residues within 4Å: Chain B: I.53, A.55, F.67, L.82, V.84, V.86, I.88, R.96, I.97, A.98, G.117, V.119, Q.144, H.146, I.148, W.185, F.226, H.228, S.236, W.240, L.243, A.253, S.254, I.255, L.274 Ligands: BCL.12, BCL.13, BCL.14, BCL.15, BCL.16, BCL.18 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:I.53, B:A.55, B:F.67, B:F.67, B:L.82, B:V.84, B:A.98, B:V.119, B:W.185, B:F.226, B:F.226, B:W.240, B:L.243, B:A.253, B:I.255, B:L.274 Hydrogen bonds: B:R.96 Metal complexes: B:H.146 BCL.18: 24 residues within 4Å: Chain B: A.41, L.42, I.71, L.82, F.186, I.187, P.189, A.190, A.193, I.194, Q.199, I.294, P.295, H.298, H.299, M.301, V.302 Chain C: Y.139 Ligands: BCL.12, BCL.13, BCL.14, BCL.15, BCL.16, BCL.17 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:L.42, B:I.71, B:F.186, B:F.186, B:I.187, B:P.189, B:A.190, B:I.194, B:P.295, B:P.295, B:M.301 Hydrogen bonds: B:Q.199 pi-Stacking: B:H.298 Metal complexes: B:H.298 BCL.23: 28 residues within 4Å: Chain A: S.127, A.129, V.130 Chain C: V.104, V.106, F.109, H.111, F.113, M.150, V.152, L.154, D.158, L.159, T.162, W.163, F.166, F.177, I.181, F.184, W.185, I.204, V.206, G.220, S.222, W.224 Ligands: BCL.24, BCL.28, BCL.29 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain A, Hydrophobic interactions: C:V.104, C:F.109, C:F.113, C:V.152, C:L.159, C:F.166, C:F.166, C:F.166, C:F.166, C:F.177, C:I.181, C:F.184, C:I.204, C:V.206, C:W.224, C:W.224, C:W.224, A:V.130 Metal complexes: C:H.111 BCL.24: 30 residues within 4Å: Chain A: Y.125, V.130, V.134, P.137, V.138, Y.139, Q.141 Chain C: L.42, P.43, L.44, C.49, I.71, S.73, V.75, N.80, K.81, L.82, V.104, V.106, F.113, F.115, M.150, F.184, W.185, I.187 Ligands: BCL.23, BCL.25, BCL.26, BCL.28, BCL.29 21 PLIP interactions: 14 interactions with chain C, 6 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: C:L.42, C:P.43, C:L.44, C:V.75, C:N.80, C:L.82, C:L.82, C:V.104, C:V.106, C:F.113, C:F.115, C:F.115, C:I.187, C:I.187, A:Y.139, A:Y.139 Hydrogen bonds: A:V.138, A:Y.139, A:Q.141 Water bridges: A:Y.125 Metal complexes: H2O.16 BCL.25: 26 residues within 4Å: Chain C: A.12, S.14, Y.16, A.34, V.38, P.39, A.40, A.41, L.42, F.186, A.190, F.259, S.261, I.266, V.268, H.299, V.302, G.303, N.306, F.308, C.354 Ligands: BCL.24, BCL.26, BCL.27, BCL.28, BCL.29 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:A.12, C:A.34, C:V.38, C:F.186, C:A.190, C:F.259, C:I.266, C:V.268, C:V.268, C:V.302, C:V.302, C:N.306, C:F.308, C:F.308, C:F.308 Hydrogen bonds: C:A.41, C:L.42 Metal complexes: C:H.299 BCL.26: 28 residues within 4Å: Chain C: Y.16, I.18, K.31, G.32, C.49, I.51, G.257, G.258, F.259, V.270, I.288, L.289, H.291, P.292, P.295, L.296, H.299, L.314, Y.346, W.349, V.350, C.354, F.361 Ligands: BCL.24, BCL.25, BCL.27, BCL.28, BCL.29 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:Y.16, C:Y.16, C:I.18, C:F.259, C:V.270, C:L.289, C:P.292, C:P.295, C:P.295, C:L.296, C:H.299, C:W.349, C:V.350 Metal complexes: C:H.291 BCL.27: 25 residues within 4Å: Chain C: I.30, I.51, I.53, A.55, V.65, F.67, I.71, I.88, D.235, R.239, E.242, L.243, F.244, P.245, L.249, I.255, L.274, P.275, G.276, L.289, P.292 Ligands: BCL.25, BCL.26, BCL.28, BCL.29 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:I.51, C:I.53, C:A.55, C:I.71, C:I.88, C:L.243, C:L.243, C:F.244, C:L.249, C:I.255, C:I.255, C:L.274, C:P.275, C:L.289 Water bridges: C:D.235 Salt bridges: C:R.239 Metal complexes: C:L.243 BCL.28: 31 residues within 4Å: Chain C: I.53, A.55, F.67, L.82, V.84, V.86, I.88, R.96, I.97, A.98, G.117, V.119, Q.144, H.146, I.148, W.185, F.226, H.228, S.236, W.240, L.243, A.253, S.254, I.255, L.274 Ligands: BCL.23, BCL.24, BCL.25, BCL.26, BCL.27, BCL.29 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:I.53, C:A.55, C:F.67, C:F.67, C:L.82, C:V.84, C:A.98, C:V.119, C:W.185, C:F.226, C:F.226, C:W.240, C:L.243, C:A.253, C:I.255, C:L.274 Hydrogen bonds: C:R.96 Metal complexes: C:H.146 BCL.29: 24 residues within 4Å: Chain A: Y.139 Chain C: A.41, L.42, I.71, L.82, F.186, I.187, P.189, A.190, A.193, I.194, Q.199, I.294, P.295, H.298, H.299, M.301, V.302 Ligands: BCL.23, BCL.24, BCL.25, BCL.26, BCL.27, BCL.28 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:L.42, C:I.71, C:F.186, C:F.186, C:I.187, C:P.189, C:A.190, C:I.194, C:P.295, C:P.295, C:M.301 Hydrogen bonds: C:Q.199 pi-Stacking: C:H.298 Metal complexes: C:H.298

12 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.8: 9 residues within 4Å: Chain A: G.165, F.166, S.169, G.173, F.177, W.180, I.181 Chain B: Y.124, Y.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.169 PG4.9: 8 residues within 4Å: Chain A: V.36, N.37, R.260, S.261, D.262, G.265, I.266, E.267 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.260 PG4.10: 7 residues within 4Å: Chain A: F.308, T.309, V.310, A.347, R.348, E.351 Chain C: D.307 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Water bridges: A:V.310 Hydrogen bonds: C:D.307 PG4.11: 6 residues within 4Å: Chain A: P.46, D.76 Chain B: A.281, R.287, E.362, L.364 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.287 PG4.19: 9 residues within 4Å: Chain B: G.165, F.166, S.169, G.173, F.177, W.180, I.181 Chain C: Y.124, Y.125 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.169 PG4.20: 8 residues within 4Å: Chain B: V.36, N.37, R.260, S.261, D.262, G.265, I.266, E.267 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.260 PG4.21: 7 residues within 4Å: Chain A: D.307 Chain B: F.308, T.309, V.310, A.347, R.348, E.351 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:V.310 Hydrogen bonds: A:D.307 PG4.22: 6 residues within 4Å: Chain B: P.46, D.76 Chain C: A.281, R.287, E.362, L.364 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.287 PG4.30: 9 residues within 4Å: Chain A: Y.124, Y.125 Chain C: G.165, F.166, S.169, G.173, F.177, W.180, I.181 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.169 PG4.31: 8 residues within 4Å: Chain C: V.36, N.37, R.260, S.261, D.262, G.265, I.266, E.267 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.260 PG4.32: 7 residues within 4Å: Chain B: D.307 Chain C: F.308, T.309, V.310, A.347, R.348, E.351 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Water bridges: C:V.310 Hydrogen bonds: B:D.307 PG4.33: 6 residues within 4Å: Chain A: A.281, R.287, E.362, L.364 Chain C: P.46, D.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.287

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tronrud, D.E. et al., Reinterpretation of the electron density at the site of the eighth bacteriochlorophyll in the FMO protein from Pelodictyon phaeum. Photosynth.Res. (2012)

Release Date

2012-01-25

Peptides

bacteriochlorophyll A protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

bacteriochlorophyll A protein