SMTL ID : 4z3y.1

Active site complex BamBC of Benzoyl Coenzyme A reductase in complex with Benzoyl-CoA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

hetero-4-4-mer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: N.76, R.77, R.181, G.247, S.248, S.298, C.299, C.302, M.304, K.305, C.306, C.534 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.299, A:C.302, A:C.306, A:C.534 SF4.8: 12 residues within 4Å: Chain B: N.76, R.77, R.181, G.247, S.248, S.298, C.299, C.302, M.304, K.305, C.306, C.534 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.299, B:C.302, B:C.306, B:C.534 SF4.15: 11 residues within 4Å: Chain C: R.77, R.181, G.247, S.248, S.298, C.299, C.302, M.304, K.305, C.306, C.534 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.299, C:C.302, C:C.306, C:C.534 SF4.23: 12 residues within 4Å: Chain D: N.76, R.77, R.181, G.247, S.248, S.298, C.299, C.302, M.304, K.305, C.306, C.534 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.299, D:C.302, D:C.306, D:C.534 SF4.29: 12 residues within 4Å: Chain E: C.20, N.21, G.22, C.23, R.24, A.25, C.26, V.51, P.62, C.128, V.130, L.133 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.20, E:C.23, E:C.26, E:C.128 SF4.30: 11 residues within 4Å: Chain E: C.30, H.34, R.48, V.49, Y.64, C.113, D.114, L.115, C.116, P.122, C.124 5 PLIP interactions: 5 interactions with chain E, Salt bridges: E:D.114 Metal complexes: E:C.30, E:C.113, E:C.116, E:C.124 SF4.31: 8 residues within 4Å: Chain E: C.73, R.76, C.89, C.92, C.96, S.98, R.99 Chain F: R.93 5 PLIP interactions: 5 interactions with chain E, Salt bridges: E:D.77 Metal complexes: E:C.73, E:C.89, E:C.92, E:C.96 SF4.32: 12 residues within 4Å: Chain F: C.20, N.21, G.22, C.23, R.24, A.25, C.26, V.51, P.62, C.128, V.130, L.133 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.20, F:C.23, F:C.26, F:C.128 SF4.33: 11 residues within 4Å: Chain F: C.30, H.34, R.48, V.49, Y.64, C.113, L.115, C.116, P.122, L.123, C.124 5 PLIP interactions: 5 interactions with chain F, Salt bridges: F:D.114 Metal complexes: F:C.30, F:C.113, F:C.116, F:C.124 SF4.34: 10 residues within 4Å: Chain E: E.67, R.93 Chain F: C.73, R.76, C.89, C.92, A.94, C.96, S.98, R.99 5 PLIP interactions: 5 interactions with chain F, Salt bridges: F:D.77 Metal complexes: F:C.73, F:C.89, F:C.92, F:C.96 SF4.35: 12 residues within 4Å: Chain G: C.20, N.21, G.22, C.23, R.24, A.25, C.26, P.62, C.128, V.130, A.132, L.133 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.20, G:C.23, G:C.26, G:C.128 SF4.36: 12 residues within 4Å: Chain G: C.30, H.34, R.48, V.49, Y.64, C.113, D.114, L.115, C.116, P.122, L.123, C.124 5 PLIP interactions: 5 interactions with chain G, Salt bridges: G:D.114 Metal complexes: G:C.30, G:C.113, G:C.116, G:C.124 SF4.37: 9 residues within 4Å: Chain G: C.73, R.76, C.89, C.92, A.94, C.96, S.98, R.99 Chain H: R.93 5 PLIP interactions: 5 interactions with chain G, Salt bridges: G:D.77 Metal complexes: G:C.73, G:C.89, G:C.92, G:C.96 SF4.38: 12 residues within 4Å: Chain H: C.20, N.21, G.22, C.23, R.24, A.25, C.26, V.51, P.62, C.128, V.130, L.133 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.20, H:C.23, H:C.26, H:C.128 SF4.39: 11 residues within 4Å: Chain H: C.30, H.34, R.48, V.49, Y.64, C.113, D.114, L.115, C.116, P.122, C.124 5 PLIP interactions: 5 interactions with chain H, Salt bridges: H:D.114 Metal complexes: H:C.30, H:C.113, H:C.116, H:C.124 SF4.40: 8 residues within 4Å: Chain G: R.93 Chain H: C.73, R.76, C.89, C.92, C.96, S.98, R.99 5 PLIP interactions: 5 interactions with chain H, Salt bridges: H:D.77 Metal complexes: H:C.73, H:C.89, H:C.92, H:C.96

8 x MTE: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER(Non-covalent)

MTE.2: 19 residues within 4Å: Chain A: R.77, M.94, M.95, G.96, S.182, S.183, S.248, K.321, C.322, Q.459, D.528, D.529, Q.533, C.534, A.535 Ligands: MTE.3, W.4, MG.5, UNL.6 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:R.77, A:R.77, A:G.96, A:S.182, A:S.183, A:S.248, A:Q.459, A:Q.533, A:A.535 Salt bridges: A:R.77, A:K.321, A:D.529 MTE.3: 22 residues within 4Å: Chain A: S.93, M.94, E.178, S.183, A.184, S.185, R.186, K.321, C.322, F.323, T.324, L.351, D.352, G.353, F.354, K.454, T.458, Q.459 Ligands: MTE.2, W.4, MG.5, UNL.6 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:M.94, A:S.176, A:S.183, A:S.185, A:S.185, A:R.186, A:L.351, A:D.352, A:D.352, A:G.353, A:F.354, A:Q.459 Salt bridges: A:E.178, A:K.454 MTE.9: 19 residues within 4Å: Chain B: R.77, M.94, M.95, G.96, S.182, S.183, S.248, K.321, C.322, Q.459, D.528, D.529, Q.533, C.534, A.535 Ligands: MTE.10, W.11, UNL.12, MG.13 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:R.77, B:R.77, B:G.96, B:S.182, B:S.183, B:S.248, B:Q.459, B:Q.533, B:A.535 Salt bridges: B:R.77, B:K.321, B:D.529 MTE.10: 19 residues within 4Å: Chain B: S.93, M.94, E.178, S.183, A.184, S.185, R.186, K.321, C.322, F.323, T.324, L.351, D.352, G.353, K.454, Q.459 Ligands: MTE.9, W.11, MG.13 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:M.94, B:M.94, B:S.183, B:S.185, B:S.185, B:R.186, B:L.351, B:D.352, B:D.352, B:G.353, B:Q.459 Salt bridges: B:E.178, B:K.454 MTE.16: 20 residues within 4Å: Chain C: R.77, M.94, M.95, G.96, S.182, S.183, S.248, K.321, C.322, Q.459, D.528, D.529, Q.533, C.534, A.535, F.540 Ligands: MTE.17, MG.18, UNL.19, W.20 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:R.77, C:G.96, C:S.183, C:S.248, C:Q.459, C:Q.533, C:A.535 Salt bridges: C:R.77, C:K.321, C:D.529 MTE.17: 22 residues within 4Å: Chain C: S.93, M.94, S.176, E.178, S.183, A.184, S.185, R.186, K.321, C.322, F.323, T.324, L.351, D.352, G.353, F.354, K.454, T.458, Q.459 Ligands: MTE.16, MG.18, W.20 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:M.94, C:S.176, C:S.183, C:S.185, C:S.185, C:R.186, C:K.321, C:L.351, C:D.352, C:G.353, C:Q.459 Salt bridges: C:E.178, C:K.454 MTE.24: 19 residues within 4Å: Chain D: R.77, M.94, M.95, G.96, S.182, S.183, S.248, K.321, C.322, Q.459, D.528, D.529, Q.533, C.534, A.535 Ligands: UNL.22, MTE.25, W.26, MG.27 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:R.77, D:R.77, D:G.96, D:S.183, D:S.248, D:Q.459, D:Q.533, D:A.535 Salt bridges: D:R.77, D:K.321, D:D.529 MTE.25: 22 residues within 4Å: Chain D: S.93, M.94, E.178, S.183, A.184, S.185, R.186, K.321, C.322, F.323, T.324, L.351, D.352, G.353, F.354, K.454, T.458, Q.459 Ligands: UNL.22, MTE.24, W.26, MG.27 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:M.94, D:S.176, D:S.183, D:S.185, D:S.185, D:R.186, D:L.351, D:D.352, D:G.353, D:F.354, D:Q.459 Salt bridges: D:E.178, D:K.454

4 x W: TUNGSTEN ION(Non-covalent)

W.4: 4 residues within 4Å: Chain A: C.322 Ligands: MTE.2, MTE.3, UNL.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.322 W.11: 4 residues within 4Å: Chain B: C.322 Ligands: MTE.9, MTE.10, UNL.12 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.322 W.20: 4 residues within 4Å: Chain C: C.322 Ligands: MTE.16, MTE.17, UNL.19 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:C.322 W.26: 4 residues within 4Å: Chain D: C.322 Ligands: UNL.22, MTE.24, MTE.25 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:C.322

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain A: M.94, S.183, S.185 Ligands: MTE.2, MTE.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:M.94, A:S.183, MTE.3 MG.13: 4 residues within 4Å: Chain B: M.94, S.183 Ligands: MTE.9, MTE.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:M.94, B:S.183, MTE.10 MG.18: 6 residues within 4Å: Chain C: M.94, S.183, A.184, S.185 Ligands: MTE.16, MTE.17 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:M.94, C:S.183, MTE.17 MG.27: 5 residues within 4Å: Chain D: M.94, S.183, S.185 Ligands: MTE.24, MTE.25 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:M.94, D:S.183, MTE.25

4 x UNL: UNKNOWN LIGAND

UNL.6: 7 residues within 4Å: Chain A: P.249, C.322, T.458 Ligands: MTE.2, MTE.3, W.4, BYC.7 No protein-ligand interaction detected (PLIP) UNL.12: 7 residues within 4Å: Chain B: P.249, C.322, T.458, F.540 Ligands: MTE.9, W.11, BYC.14 No protein-ligand interaction detected (PLIP) UNL.19: 6 residues within 4Å: Chain C: P.249, C.322, T.458 Ligands: MTE.16, W.20, BYC.21 No protein-ligand interaction detected (PLIP) UNL.22: 7 residues within 4Å: Chain D: P.249, C.322, T.458 Ligands: MTE.24, MTE.25, W.26, BYC.28 No protein-ligand interaction detected (PLIP)

4 x BYC: benzoyl coenzyme A(Non-covalent)

BYC.7: 26 residues within 4Å: Chain A: P.249, E.251, W.259, H.260, F.264, R.272, C.322, F.323, L.434, L.436, L.438, S.439, M.440, N.442, Y.445, I.457, T.458, E.461, Q.466, A.467, P.499, R.500, S.504, M.505, F.540 Ligands: UNL.6 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:P.249, A:F.264, A:F.323, A:F.323, A:Y.445, A:T.458, A:A.467 Hydrogen bonds: A:R.272, A:S.439, A:S.439, A:S.439, A:M.440, A:Y.445, A:Q.466, A:R.500, A:R.500, A:S.504, A:S.504 pi-Cation interactions: A:R.500, A:R.500 BYC.14: 23 residues within 4Å: Chain B: P.249, E.251, W.259, H.260, F.264, C.322, F.323, L.434, L.436, L.438, S.439, M.440, Y.445, I.457, T.458, E.461, Q.466, A.467, R.500, S.504, M.505, F.540 Ligands: UNL.12 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:P.249, B:F.264, B:F.323, B:F.323, B:Y.445, B:T.458, B:A.467 Hydrogen bonds: B:R.272, B:S.439, B:S.439, B:S.439, B:M.440, B:Y.445, B:Q.466, B:R.500, B:S.504, B:S.504 pi-Cation interactions: B:R.500, B:R.500 BYC.21: 26 residues within 4Å: Chain C: L.243, P.249, E.251, W.259, H.260, F.264, R.272, C.322, F.323, L.434, L.436, L.438, S.439, M.440, Y.445, I.457, T.458, E.461, Q.466, A.467, P.499, R.500, S.504, M.505, F.540 Ligands: UNL.19 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:P.249, C:F.323, C:Y.445, C:A.467 Hydrogen bonds: C:R.272, C:S.439, C:S.439, C:S.439, C:M.440, C:Y.445, C:Q.466, C:S.504, C:S.504 pi-Cation interactions: C:R.500, C:R.500 BYC.28: 24 residues within 4Å: Chain D: P.249, E.251, W.259, H.260, F.264, C.322, F.323, L.434, L.436, L.438, S.439, M.440, N.442, Y.445, I.457, T.458, E.461, Q.466, A.467, R.500, S.504, M.505, F.540 Ligands: UNL.22 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:P.249, D:F.264, D:F.323, D:F.323, D:Y.445, D:T.458, D:A.467 Hydrogen bonds: D:R.272, D:S.439, D:S.439, D:M.440, D:Y.445, D:Q.466, D:S.504, D:S.504 pi-Cation interactions: D:R.500, D:R.500

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weinert, T. et al., Structural basis of enzymatic benzene ring reduction. Nat.Chem.Biol. (2015)

Release Date

2015-07-01

Peptides

Benzoyl-CoA reductase, putative: ABCD
Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Benzoyl-CoA reductase, putative

Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein

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