SMTL ID : 6n96.1

Methylmalonyl-CoA decarboxylase in complex with 2-sulfonate-propionyl-oxa(dethia)-CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-hexamer

Ligands

8 x LCV: (2~{S})-1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethoxy]-1-oxidanylidene-propane-2-sulfonic acid(Non-covalent)(Covalent)

LCV.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: SO5.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.71, A:W.108, A:W.108, A:L.136, A:V.138 Hydrogen bonds: A:A.64, A:H.66, A:H.66, A:I.68, A:G.110, A:T.132 Water bridges: A:H.69, A:K.253, A:K.253 Salt bridges: A:K.60, A:K.253 pi-Stacking: A:F.250, A:F.250 LCV.3: 21 residues within 4Å: Chain B: 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: SO5.4 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:H.66, B:L.71, B:W.108, B:L.136, B:V.138 Hydrogen bonds: B:A.64, B:H.66, B:H.66, B:I.68, B:G.110, B:T.132 Water bridges: B:K.60 Salt bridges: B:K.60, B:K.253 pi-Stacking: B:F.250, B:F.250 LCV.5: 22 residues within 4Å: Chain C: R.23, K.24, L.25, 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: SO5.6 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: 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 Water bridges: C:K.60 Salt bridges: C:K.24, C:K.60, C:K.253 LCV.7: 9 residues within 4Å: Chain B: H.197 Chain C: S.106, V.107, W.108, T.128, F.129, S.130, S.165, P.166 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:V.107, C:T.128, C:T.128, C:S.130, C:S.165 Water bridges: C:N.135, B:K.201 pi-Stacking: C:W.108 Salt bridges: B:H.197, B:H.197 LCV.8: 20 residues within 4Å: Chain D: 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: SO5.9 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:L.71, D:W.108, D:W.108, D:L.136, D:V.138 Hydrogen bonds: D:A.64, D:H.66, D:H.66, D:I.68, D:G.110, D:T.132 Salt bridges: D:K.60, D:K.253 pi-Stacking: D:F.250, D:F.250 LCV.11: 20 residues within 4Å: Chain E: L.25, 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: SO5.12 17 PLIP interactions: 17 interactions with chain E Hydrophobic interactions: E:A.64, E:L.71, E:W.108, E:W.108, E:L.136, E:V.138 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 LCV.13: 20 residues within 4Å: Chain F: L.25, V.61, 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: SO5.14 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:V.61, F:H.66, F:W.108, F:W.108 Hydrogen bonds: F:A.64, F:H.66, F:H.66, F:D.67, F:I.68, F:G.110, F:T.132, F:K.253 Salt bridges: F:K.253 pi-Stacking: F:F.250, F:F.250 LCV.15: 10 residues within 4Å: Chain E: H.197 Chain F: S.106, V.107, W.108, T.128, F.129, S.130, S.165, P.166, K.255 11 PLIP interactions: 3 interactions with chain E, 8 interactions with chain F Water bridges: E:K.201, F:N.135, F:N.135 Salt bridges: E:H.197, E:H.197, F:K.255 Hydrogen bonds: F:V.107, F:T.128, F:F.129, F:S.130, F:S.165

6 x SO5: (2~{R})-1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethoxy]-1-oxidanylidene-propane-2-sulfonic acid(Non-covalent)

SO5.2: 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: LCV.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 Water bridges: A:H.69, A:K.253, A:K.253 Salt bridges: A:K.60, A:K.253 pi-Stacking: A:F.250, A:F.250 SO5.4: 20 residues within 4Å: Chain B: 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: LCV.3 15 PLIP interactions: 15 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 Water bridges: B:K.60, B:K.60 Salt bridges: B:K.60, B:K.253 pi-Stacking: B:F.250, B:F.250 SO5.6: 21 residues within 4Å: Chain C: R.23, K.24, L.25, 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: LCV.5 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: 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 Salt bridges: C:K.24, C:K.60, C:K.253 SO5.9: 19 residues within 4Å: Chain D: L.25, K.60, 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: LCV.8 14 PLIP interactions: 14 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:H.66, D:I.68, D:G.110, D:T.132 Salt bridges: D:K.60, D:K.253 pi-Stacking: D:F.250, D:F.250 SO5.12: 19 residues within 4Å: Chain E: L.25, 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: LCV.11 16 PLIP interactions: 16 interactions with chain E Hydrophobic interactions: 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 SO5.14: 19 residues within 4Å: Chain F: L.25, 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: LCV.13 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:H.66, F:W.108, F:Y.140 Hydrogen bonds: F:A.64, F:H.66, F:H.66, F:D.67, F:I.68, F:G.110, F:T.132, F:K.253 Salt bridges: F:K.60, F:K.253 pi-Stacking: F:F.250, F:F.250

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.10: 6 residues within 4Å: Chain D: V.9, I.11, V.14, V.16, L.192, H.196 No protein-ligand interaction detected (PLIP)

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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