SMTL ID : 6n92.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-hexamer

Ligands

9 x KFV: [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]ethylsulfanyl]-1-oxidanylidene-propan-2-ylidene]-bis(oxidanidyl)azanium(Non-covalent)(Covalent)

KFV.1: 20 residues within 4Å: Chain A: L.25, K.60, A.64, G.65, H.66, D.67, I.68, H.69, L.79, L.85, W.108, G.109, G.110, T.132, P.133, L.136, V.138, Y.140, F.250, K.253 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:A.64, A:H.66, A:L.85, 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:K.253 Water bridges: A:N.135 Salt bridges: A:K.60, A:K.253 pi-Stacking: A:F.250, A:F.250 KFV.3: 16 residues within 4Å: Chain B: R.23, K.24, L.25, A.64, H.66, D.67, I.68, L.71, P.78, W.108, T.132, P.133, L.136, V.138, Y.140, F.250 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:P.78, B:W.108, B:V.138 Hydrogen bonds: B:A.64, B:H.66, B:H.66, B:I.68 Salt bridges: B:K.24 KFV.4: 17 residues within 4Å: Chain C: R.23, K.24, L.25, A.64, H.66, D.67, I.68, H.69, L.71, W.108, T.132, P.133, L.136, V.138, Y.140, F.250, K.253 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.71, C:W.108, C:V.138 Hydrogen bonds: C:A.64, C:H.66, C:H.66, C:D.67, C:I.68 Salt bridges: C:K.24 KFV.6: 11 residues within 4Å: Chain B: H.197 Chain C: S.106, V.107, W.108, T.128, F.129, S.130, T.163, A.164, S.165, P.166 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:V.107, C:T.128, C:S.130 Water bridges: C:S.165, B:K.201, B:K.201, B:K.201 pi-Stacking: C:W.108, C:W.108 Salt bridges: B:H.197 KFV.9: 14 residues within 4Å: Chain D: L.25, K.60, V.61, A.64, G.65, H.66, D.67, I.68, L.71, W.108, T.132, L.136, F.250, K.253 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:W.108, D:W.108 Hydrogen bonds: D:H.66, D:I.68, D:T.132 Water bridges: D:H.66, D:N.135 Salt bridges: D:K.60, D:K.253 pi-Stacking: D:F.250 KFV.11: 18 residues within 4Å: Chain E: R.23, K.24, L.25, V.61, A.64, G.65, H.66, D.67, I.68, H.69, W.108, G.109, G.110, T.132, P.133, V.138, Y.140, F.250 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:L.25, E:V.61, E:H.66, 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 Salt bridges: E:K.24 KFV.12: 9 residues within 4Å: Chain D: H.197 Chain E: S.106, V.107, W.108, T.128, F.129, S.130, S.165, P.166 18 PLIP interactions: 5 interactions with chain D, 13 interactions with chain E Water bridges: D:K.201, D:K.201, D:K.201, E:N.135, E:N.135, E:N.135, E:A.164, E:S.165 Salt bridges: D:H.197, D:H.197 Hydrogen bonds: E:V.107, E:T.128, E:T.128, E:T.128, E:S.130, E:S.165 pi-Stacking: E:W.108, E:W.108 KFV.13: 18 residues within 4Å: Chain F: R.23, K.24, L.25, V.61, A.64, G.65, H.66, D.67, I.68, L.85, W.108, G.109, G.110, T.132, P.133, V.138, Y.140, F.250 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:L.25, F:V.61, F:A.64, F:L.85, F:W.108, F:Y.140 Hydrogen bonds: F:A.64, F:H.66, F:H.66, F:H.66, F:D.67, F:I.68, F:G.110, F:T.132 Water bridges: F:N.135 KFV.15: 9 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 10 PLIP interactions: 7 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:V.107, F:T.128, F:T.128, F:T.128, F:S.130 pi-Stacking: F:W.108, F:W.108 Water bridges: E:K.201, E:K.201 Salt bridges: E:H.197

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

NI.2: 3 residues within 4Å: Chain A: H.220 Chain B: H.220 Chain C: H.220 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: A:H.220, B:H.220, C:H.220, H2O.8, H2O.35, H2O.36 NI.8: 3 residues within 4Å: Chain D: H.220 Chain E: H.220 Chain F: H.220 6 PLIP interactions: 1 interactions with chain F, 1 interactions with chain D, 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: F:H.220, D:H.220, E:H.220, H2O.49, H2O.74, H2O.75 NI.14: 4 residues within 4Å: Chain F: E.241, H.261 Ligands: KG7.16, IMD.17 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.241, F:H.261, H2O.73

1 x K: POTASSIUM ION(Non-covalent)

K.5: 2 residues within 4Å: Chain C: Q.38 Ligands: PG4.7 No protein-ligand interaction detected (PLIP)

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

PG4.7: 5 residues within 4Å: Chain C: D.34, M.37, Q.38, S.41 Ligands: K.5 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.38, C:S.41

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.10: 7 residues within 4Å: Chain D: V.9, T.10, I.11, V.14, V.16, L.192, H.196 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:I.11 IMD.17: 5 residues within 4Å: Chain F: E.241, V.259, H.261 Ligands: NI.14, KG7.16 1 PLIP interactions: 1 interactions with chain F Water bridges: F:E.241

1 x KG7: (2E)-2-(hydroxyimino)propanoic acid(Non-covalent)

KG7.16: 4 residues within 4Å: Chain F: E.241, H.261 Ligands: NI.14, IMD.17 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:E.241 Water bridges: F:E.241, F:H.261 Salt bridges: F:H.261

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

Related Entries With Identical Sequence