SMTL ID : 4z40.1 (1 other biounit)

Active site complex BamBC of Benzoyl Coenzyme A reductase as isolated

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-2-2-mer

Ligands

2 x UNL: UNKNOWN LIGAND

UNL.1: 5 residues within 4Å: Chain A: P.249, C.322, T.458 Ligands: MTE.3, W.5 No protein-ligand interaction detected (PLIP) UNL.8: 6 residues within 4Å: Chain B: P.249, C.322, T.458, F.540 Ligands: MTE.10, W.12 No protein-ligand interaction detected (PLIP)

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

SF4.2: 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 SF4.9: 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: 12 residues within 4Å: Chain C: 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 C, Metal complexes: C:C.20, C:C.23, C:C.26, C:C.128 SF4.16: 11 residues within 4Å: Chain C: 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 C, Salt bridges: C:D.114 Metal complexes: C:C.30, C:C.113, C:C.116, C:C.124 SF4.17: 8 residues within 4Å: Chain C: C.73, C.89, C.92, A.94, C.96, S.98, R.99 Chain D: R.93 5 PLIP interactions: 5 interactions with chain C, Salt bridges: C:D.77 Metal complexes: C:C.73, C:C.89, C:C.92, C:C.96 SF4.18: 12 residues within 4Å: Chain D: 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 D, Metal complexes: D:C.20, D:C.23, D:C.26, D:C.128 SF4.19: 12 residues within 4Å: Chain D: 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 D, Salt bridges: D:D.114 Metal complexes: D:C.30, D:C.113, D:C.116, D:C.124 SF4.20: 9 residues within 4Å: Chain C: R.93 Chain D: T.69, C.73, C.89, C.92, A.94, C.96, S.98, R.99 5 PLIP interactions: 5 interactions with chain D, Salt bridges: D:D.77 Metal complexes: D:C.73, D:C.89, D:C.92, D:C.96

4 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.3: 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: UNL.1, MTE.4, W.5, MG.6 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:R.77, A:R.77, A:G.96, A:R.181, A:S.183, A:Q.459, A:H.525, A:Q.533, A:A.535 Salt bridges: A:R.77, A:K.321, A:D.529 MTE.4: 20 residues within 4Å: Chain A: S.93, M.94, S.176, E.178, S.183, A.184, S.185, R.186, K.321, C.322, T.324, L.351, D.352, G.353, F.354, K.454, Q.459 Ligands: MTE.3, W.5, MG.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:S.185, A:R.186, A:L.351, A:D.352, A:G.353, A:Q.459, A:Q.459 Salt bridges: A:E.178, A:K.454 MTE.10: 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: UNL.8, MTE.11, W.12, MG.13 14 PLIP interactions: 14 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 Water bridges: B:G.97, B:G.97 Salt bridges: B:R.77, B:K.321, B:D.529 MTE.11: 21 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, F.354, K.454, T.458, Q.459 Ligands: MTE.10, W.12, MG.13 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: 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:F.354, B:Q.459, B:Q.459 Water bridges: B:S.183, B:T.347 Salt bridges: B:E.178, B:K.454

2 x W: TUNGSTEN ION(Non-covalent)

W.5: 4 residues within 4Å: Chain A: C.322 Ligands: UNL.1, MTE.3, MTE.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.322 W.12: 4 residues within 4Å: Chain B: C.322 Ligands: UNL.8, MTE.10, MTE.11 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.322

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 5 residues within 4Å: Chain A: M.94, M.95, S.183 Ligands: MTE.3, MTE.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:M.94, A:S.183, MTE.4 MG.13: 5 residues within 4Å: Chain B: M.94, S.183, S.185 Ligands: MTE.10, MTE.11 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:M.94, B:S.183, MTE.11

2 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain A: E.251, H.255, E.257, H.260 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.251, A:E.251, A:H.255, A:E.257, A:H.260 ZN.14: 4 residues within 4Å: Chain B: E.251, H.255, E.257, H.260 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.251, B:E.251, B:H.255, B:E.257, B:H.260

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

2015-06-24

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
E

D
F

Benzoyl-CoA reductase, putative

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

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