SMTL ID : 1on9.1 (1 other biounit)

Transcarboxylase 12S crystal structure: hexamer assembly and substrate binding to a multienzyme core (with hydrolyzed methylmalonyl-coenzyme a bound)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

3 x CD: CADMIUM ION(Non-covalent)

CD.1: 2 residues within 4Å: Chain A: H.387 Chain D: H.387 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: A:H.387, D:H.387, H2O.1, H2O.1, H2O.16, H2O.81 CD.3: 2 residues within 4Å: Chain B: H.387 Chain E: H.387 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: B:H.387, E:H.387, H2O.22, H2O.32, H2O.104, H2O.104 CD.5: 2 residues within 4Å: Chain C: H.387 Chain F: H.387 6 PLIP interactions: 1 interactions with chain F, 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: F:H.387, C:H.387, H2O.46, H2O.46, H2O.110, H2O.119

6 x MCA: METHYLMALONYL-COENZYME A(Non-covalent)

MCA.2: 10 residues within 4Å: Chain A: R.33, R.34, F.104, M.107, G.108, S.110, G.140, G.141, A.142, Q.145 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.33, A:S.110, A:G.140 Water bridges: A:R.34, A:M.107, A:G.108, A:I.144, A:Q.145 Salt bridges: A:R.34 MCA.4: 7 residues within 4Å: Chain B: R.34, F.104, M.107, G.108, S.110, G.140, A.142 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.110, B:A.142 Water bridges: B:R.34, B:R.34, B:G.108, B:G.108, B:I.144 Salt bridges: B:R.34 MCA.6: 9 residues within 4Å: Chain C: R.33, R.34, K.37, F.104, M.107, G.108, S.110, G.140, A.142 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:S.110, C:G.140 Water bridges: C:R.34, C:R.34, C:K.37, C:K.37, C:K.37, C:G.108, C:I.144, C:Q.145, C:Q.145, C:Q.145 Salt bridges: C:R.33, C:R.34, C:K.37 MCA.7: 9 residues within 4Å: Chain D: R.33, R.34, K.37, F.104, M.107, G.108, S.110, G.140, A.142 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:S.110, D:G.140 Water bridges: D:R.34, D:R.34, D:R.34, D:G.108, D:I.144, D:Q.145 Salt bridges: D:R.33, D:R.34, D:K.37 MCA.8: 10 residues within 4Å: Chain E: R.33, R.34, K.37, F.104, M.107, G.108, S.110, G.140, G.141, A.142 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:R.33, E:K.37, E:S.110, E:A.142 Water bridges: E:R.34, E:R.34, E:K.37, E:G.108, E:G.108, E:G.108, E:I.144 Salt bridges: E:R.34 MCA.9: 9 residues within 4Å: Chain F: R.33, R.34, K.37, F.104, M.107, G.108, S.110, G.140, A.142 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:S.110, F:G.140 Water bridges: F:R.33, F:R.34, F:K.37, F:K.37, F:K.37, F:K.37, F:K.37, F:G.108, F:I.144, F:Q.145 Salt bridges: F:R.33, F:R.34, F:K.37

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.10: 4 residues within 4Å: Chain F: K.250, N.267, W.302, D.304 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:W.302 Hydrogen bonds: F:N.267 Water bridges: F:V.266, F:R.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hall, P.R. et al., Transcarboxylase 12S crystal structure: hexamer assembly and substrate binding to a multienzyme core. Embo J. (2003)

Release Date

2003-05-20

Peptides

Methylmalonyl-CoA carboxyltransferase 12S subunit: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Methylmalonyl-CoA carboxyltransferase 12S subunit

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