SMTL ID : 6n95.1

Methylmalonyl-CoA decarboxylase in complex with 2-sulfonate-propionyl-CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

6 x YXS: (2S)-sulfonatepropionyl-CoA(Non-covalent)

YXS.1: 22 residues within 4Å: Chain A: K.24, L.25, K.60, A.64, G.65, H.66, D.67, I.68, H.69, L.71, W.108, G.109, G.110, M.131, T.132, P.133, L.136, V.138, Y.140, F.250, K.253 Ligands: YXR.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.71, A:W.108, A:W.108, A:V.138 Hydrogen bonds: A:A.64, A:H.66, A:H.66, A:I.68, A:G.110, A:T.132, A:K.253, A:K.253 Salt bridges: A:K.60, A:K.253 pi-Stacking: A:F.250, A:F.250 YXS.4: 20 residues within 4Å: Chain B: L.25, K.60, A.64, G.65, H.66, D.67, I.68, L.71, W.108, G.109, G.110, M.131, T.132, P.133, L.136, V.138, Y.140, F.250, K.253 Ligands: YXR.5 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.71, B:W.108, B:W.108, B:V.138 Hydrogen bonds: B:A.64, B:H.66, B:H.66, B:I.68, B:G.110, B:T.132, B:K.253, B:K.253 Salt bridges: B:K.60, B:K.253 pi-Stacking: B:F.250, B:F.250 YXS.6: 22 residues within 4Å: Chain C: R.23, K.24, L.25, A.27, V.61, A.64, G.65, H.66, D.67, I.68, L.71, W.108, G.109, G.110, M.131, T.132, P.133, L.136, V.138, Y.140, F.250 Ligands: YXR.7 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:V.61, C:L.71, C:W.108, C:W.108, C:V.138 Hydrogen bonds: C:A.64, C:H.66, C:H.66, C:D.67, C:I.68, C:G.110, C:T.132, C:T.132 Salt bridges: C:K.24 YXS.12: 20 residues within 4Å: Chain D: L.25, K.60, A.64, G.65, H.66, D.67, I.68, H.69, W.108, G.109, G.110, M.131, T.132, P.133, L.136, V.138, Y.140, F.250, K.253 Ligands: YXR.13 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:W.108, D:W.108, D:V.138 Hydrogen bonds: D:A.64, D:G.65, D:H.66, D:I.68, D:G.110, D:T.132, D:T.132, D:K.253 Water bridges: D:H.69 Salt bridges: D:K.60, D:K.253 pi-Stacking: D:F.250, D:F.250 YXS.14: 22 residues within 4Å: Chain E: K.24, L.25, A.27, K.60, A.64, G.65, H.66, D.67, I.68, H.69, L.71, W.108, G.109, G.110, M.131, T.132, P.133, L.136, V.138, Y.140, F.250 Ligands: YXR.15 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:H.66, E:L.71, E:W.108, E:W.108 Hydrogen bonds: E:A.64, E:H.66, E:H.66, E:D.67, E:I.68, E:G.110, E:T.132 Salt bridges: E:K.24, E:K.60 YXS.16: 22 residues within 4Å: Chain F: K.24, L.25, A.27, K.60, V.61, A.64, G.65, H.66, D.67, I.68, L.71, W.108, G.109, G.110, M.131, T.132, P.133, L.136, V.138, Y.140, F.250 Ligands: YXR.17 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:V.61, F:H.66, F:L.71, F:W.108, F:W.108, F:V.138 Hydrogen bonds: F:A.64, F:H.66, F:H.66, F:D.67, F:I.68, F:G.110, F:T.132, F:T.132 Salt bridges: F:K.60

6 x YXR: (2R)-sulfonatepropionyl-CoA(Non-covalent)

YXR.2: 21 residues within 4Å: Chain A: K.24, L.25, K.60, A.64, G.65, H.66, D.67, I.68, H.69, W.108, G.109, G.110, M.131, T.132, P.133, L.136, V.138, Y.140, F.250, K.253 Ligands: YXS.1 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:H.66, A:W.108, A:W.108, A:Y.140 Hydrogen bonds: A:A.64, A:H.66, A:H.66, A:I.68, A:G.110, A:T.132, A:T.132, A:K.253, A:K.253 Salt bridges: A:K.60, A:K.253 pi-Stacking: A:F.250, A:F.250 YXR.5: 20 residues within 4Å: Chain B: L.25, K.60, V.61, A.64, G.65, H.66, D.67, I.68, W.108, G.109, G.110, M.131, T.132, P.133, L.136, V.138, Y.140, F.250, K.253 Ligands: YXS.4 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:H.66, B:W.108, B:Y.140 Hydrogen bonds: B:A.64, B:H.66, B:H.66, B:I.68, B:G.110, B:T.132, B:T.132, B:K.253, B:K.253 Salt bridges: B:K.60, B:K.253 pi-Stacking: B:F.250, B:F.250 YXR.7: 21 residues within 4Å: Chain C: R.23, K.24, L.25, A.27, V.61, A.64, G.65, H.66, D.67, I.68, W.108, G.109, G.110, M.131, T.132, P.133, L.136, V.138, Y.140, F.250 Ligands: YXS.6 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:V.61, C:H.66, C:W.108, C:W.108, C:Y.140 Hydrogen bonds: C:A.64, C:H.66, C:H.66, C:D.67, C:I.68, C:G.110, C:T.132, C:T.132, C:T.132 Salt bridges: C:K.24 YXR.13: 20 residues within 4Å: Chain D: K.24, L.25, K.60, A.64, G.65, H.66, D.67, I.68, H.69, W.108, G.109, G.110, M.131, T.132, P.133, L.136, V.138, Y.140, F.250 Ligands: YXS.12 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:H.66, D:W.108, D:W.108, D:Y.140 Hydrogen bonds: D:A.64, D:H.66, D:I.68, D:G.110 Water bridges: D:K.24, D:K.24, D:H.69 Salt bridges: D:K.24, D:K.60 YXR.15: 19 residues within 4Å: Chain E: L.25, K.60, A.64, H.66, D.67, I.68, H.69, W.108, G.109, G.110, M.131, T.132, P.133, L.136, V.138, Y.140, F.250, K.253 Ligands: YXS.14 17 PLIP interactions: 17 interactions with chain E Hydrophobic interactions: E:L.25, E:A.64, E:H.66, E:W.108, E:W.108, E:Y.140 Hydrogen bonds: E:A.64, E:H.66, E:H.66, E:D.67, E:I.68, E:G.110, E:T.132 Salt bridges: E:K.60, E:K.253 pi-Stacking: E:F.250, E:F.250 YXR.17: 20 residues within 4Å: Chain F: L.25, K.60, A.64, G.65, H.66, D.67, I.68, H.69, W.108, G.109, G.110, M.131, T.132, P.133, L.136, V.138, Y.140, F.250, K.253 Ligands: YXS.16 18 PLIP interactions: 18 interactions with chain F Hydrophobic interactions: F:H.66, F:W.108, F:W.108, F:Y.140 Hydrogen bonds: F:A.64, F:A.64, F:H.66, F:D.67, F:I.68, F:G.110, F:T.132, F:T.132, F:K.253, F:K.253 Salt bridges: F:K.60, F:K.253 pi-Stacking: F:F.250, F:F.250

2 x NI: NICKEL (II) ION(Non-covalent)

NI.3: 3 residues within 4Å: Chain A: H.220 Chain B: H.220 Chain C: H.220 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: A:H.220, B:H.220, C:H.220, H2O.19, H2O.28 NI.11: 3 residues within 4Å: Chain D: H.220 Chain E: H.220 Chain F: H.220 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: D:H.220, F:H.220, E:H.220, H2O.63

2 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.8: 2 residues within 4Å: Chain C: Q.38 Ligands: PG4.9 No protein-ligand interaction detected (PLIP) K.18: 1 residues within 4Å: Ligands: PGE.19 No protein-ligand interaction detected (PLIP)

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

PG4.9: 5 residues within 4Å: Chain C: D.34, M.37, Q.38, S.41 Ligands: K.8 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.38

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 2 residues within 4Å: Chain C: N.44, P.46 No protein-ligand interaction detected (PLIP) PEG.20: 2 residues within 4Å: Chain F: E.241, H.261 No protein-ligand interaction detected (PLIP)

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.19: 4 residues within 4Å: Chain F: F.190, Q.193, M.194 Ligands: K.18 1 PLIP interactions: 1 interactions with chain D Water bridges: D:S.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stunkard, L.M. et al., Sulfonate/Nitro Bearing Methylmalonyl-Thioester Isosteres Applied to Methylmalonyl-CoA Decarboxylase Structure-Function Studies. J. Am. Chem. Soc. (2019)

Release Date

2019-04-10

Peptides

Methylmalonyl-CoA decarboxylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Methylmalonyl-CoA decarboxylase

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