SMTL ID : 4zaa.1

Structure of A. niger Fdc1 in complex with 4-vinyl guaiacol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.24 Å

Oligo State

homo-dimer

Ligands

2 x 4LU: 1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-yl)-D-ribitol(Non-covalent)

4LU.1: 24 residues within 4Å: Chain A: T.153, N.168, W.169, S.170, I.171, A.172, R.173, L.185, Q.190, H.191, S.223, S.224, M.225, P.226, E.233, C.316, T.323, I.327, K.391 Ligands: FZZ.2, MN.3, K.4, 4M4.6, CO2.8 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.171, A:I.171, A:T.323, A:I.327 Hydrogen bonds: A:N.168, A:I.171, A:I.171, A:R.173, A:Q.190, A:H.191, A:S.224 Water bridges: A:S.170, A:S.170, A:I.227, A:K.391, A:K.391 Salt bridges: A:H.191, A:K.391 4LU.9: 24 residues within 4Å: Chain B: T.153, N.168, W.169, S.170, I.171, A.172, R.173, L.185, Q.190, H.191, S.223, S.224, M.225, P.226, E.233, C.316, T.323, I.327, K.391 Ligands: FZZ.10, MN.11, K.12, 4M4.14, CO2.16 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.171, B:I.171, B:T.323, B:I.327 Hydrogen bonds: B:N.168, B:I.171, B:I.171, B:R.173, B:Q.190, B:H.191, B:S.224 Water bridges: B:S.170, B:S.170, B:I.227, B:K.391, B:K.391 Salt bridges: B:H.191, B:K.391

2 x FZZ: 1-deoxy-5-O-phosphono-1-[(10aR)-2,2,3,4-tetramethyl-8,10-dioxo-1,2,8,9,10,10a-hexahydro-6H-indeno[1,7-ef]pyrimido[4,5-b][1,4]diazepin-6-yl]-D-ribitol(Non-covalent)

FZZ.2: 25 residues within 4Å: Chain A: T.153, N.168, W.169, S.170, I.171, A.172, R.173, L.185, Q.190, H.191, S.223, S.224, M.225, P.226, E.233, S.314, C.316, T.323, I.327, K.391 Ligands: 4LU.1, MN.3, K.4, 4M4.6, CO2.8 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:I.171, A:I.171, A:T.323, A:I.327 Hydrogen bonds: A:N.168, A:W.169, A:I.171, A:I.171, A:R.173, A:Q.190, A:H.191, A:S.224 Water bridges: A:S.170, A:I.192, A:I.227, A:K.391, A:K.391 Salt bridges: A:H.191, A:K.391 FZZ.10: 25 residues within 4Å: Chain B: T.153, N.168, W.169, S.170, I.171, A.172, R.173, L.185, Q.190, H.191, S.223, S.224, M.225, P.226, E.233, S.314, C.316, T.323, I.327, K.391 Ligands: 4LU.9, MN.11, K.12, 4M4.14, CO2.16 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:I.171, B:I.171, B:T.323, B:I.327 Hydrogen bonds: B:N.168, B:W.169, B:I.171, B:I.171, B:R.173, B:Q.190, B:H.191, B:S.224 Water bridges: B:S.170, B:I.192, B:I.227, B:K.391, B:K.391 Salt bridges: B:H.191, B:K.391

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 6 residues within 4Å: Chain A: N.168, H.191, E.233 Ligands: 4LU.1, FZZ.2, K.4 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.191, A:E.233, H2O.1, H2O.5, 4LU.1 MN.11: 6 residues within 4Å: Chain B: N.168, H.191, E.233 Ligands: 4LU.9, FZZ.10, K.12 5 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: B:H.191, B:E.233, 4LU.9, H2O.19, H2O.23

4 x K: POTASSIUM ION(Non-covalent)

K.4: 8 residues within 4Å: Chain A: W.169, A.222, S.223, M.225, E.233 Ligands: 4LU.1, FZZ.2, MN.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:A.222, A:M.225, A:E.233, 4LU.1 K.5: 4 residues within 4Å: Chain A: R.421, D.427, D.459, L.461 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:R.421, A:D.427, A:D.459, A:L.461, H2O.31 K.12: 8 residues within 4Å: Chain B: W.169, A.222, S.223, M.225, E.233 Ligands: 4LU.9, FZZ.10, MN.11 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:A.222, B:M.225, B:E.233, 4LU.9 K.13: 4 residues within 4Å: Chain B: R.421, D.427, D.459, L.461 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:R.421, B:D.427, B:D.459, B:L.461, H2O.13

4 x 4M4: 2-Methoxy-4-vinylphenol(Non-covalent)

4M4.6: 11 residues within 4Å: Chain A: L.185, I.187, P.188, Q.190, Y.394, T.395, F.437, L.439 Ligands: 4LU.1, FZZ.2, CO2.8 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.185, A:Y.394, A:T.395, A:F.437, A:F.437, A:L.439 Hydrogen bonds: A:Q.190, A:Q.190, A:Y.394 4M4.7: 7 residues within 4Å: Chain A: P.5, A.6, E.15, A.16, V.19, D.20, R.86 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.6, A:A.16, A:V.19 Hydrogen bonds: A:A.6 Water bridges: A:Q.4 4M4.14: 11 residues within 4Å: Chain B: L.185, I.187, P.188, Q.190, Y.394, T.395, F.437, L.439 Ligands: 4LU.9, FZZ.10, CO2.16 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.185, B:Y.394, B:T.395, B:F.437, B:F.437, B:L.439 Hydrogen bonds: B:Q.190, B:Q.190, B:Y.394 4M4.15: 7 residues within 4Å: Chain B: P.5, A.6, E.15, A.16, V.19, D.20, R.86 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.6, B:A.16, B:V.19 Hydrogen bonds: B:A.6 Water bridges: B:Q.4

2 x CO2: CARBON DIOXIDE(Non-covalent)

CO2.8: 8 residues within 4Å: Chain A: R.173, F.280, E.282, M.283, L.439 Ligands: 4LU.1, FZZ.2, 4M4.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.173, A:M.283 CO2.16: 8 residues within 4Å: Chain B: R.173, F.280, E.282, M.283, L.439 Ligands: 4LU.9, FZZ.10, 4M4.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.173, B:M.283

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Payne, K.A. et al., New cofactor supports alpha , beta-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition. Nature (2015)

Release Date

2015-06-17

Peptides

fdc1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

fdc1

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