SMTL ID : 1on3.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-12-mer

Ligands

6 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 D, 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: D:H.387, A:H.387, H2O.10, H2O.10, H2O.74, H2O.74 CD.5: 2 residues within 4Å: Chain B: H.387 Chain E: H.387 6 PLIP interactions: 1 interactions with chain E, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: E:H.387, B:H.387, H2O.31, H2O.92, H2O.94, H2O.96 CD.9: 2 residues within 4Å: Chain C: H.387 Chain F: H.387 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: C:H.387, F:H.387, H2O.53, H2O.53, H2O.117, H2O.117 CD.19: 2 residues within 4Å: Chain G: H.387 Chain J: H.387 6 PLIP interactions: 1 interactions with chain J, 1 interactions with chain G, 4 Ligand-Water interactions Metal complexes: J:H.387, G:H.387, H2O.139, H2O.139, H2O.203, H2O.204 CD.23: 2 residues within 4Å: Chain H: H.387 Chain K: H.387 6 PLIP interactions: 1 interactions with chain H, 1 interactions with chain K, 4 Ligand-Water interactions Metal complexes: H:H.387, K:H.387, H2O.161, H2O.222, H2O.223, H2O.225 CD.27: 2 residues within 4Å: Chain I: H.387 Chain L: H.387 6 PLIP interactions: 1 interactions with chain I, 1 interactions with chain L, 4 Ligand-Water interactions Metal complexes: I:H.387, L:H.387, H2O.182, H2O.182, H2O.247, H2O.247

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

MCA.2: 20 residues within 4Å: Chain A: R.34, F.104, M.107, G.108, S.110, G.140, G.141, A.142, R.143, I.144, Q.145, P.177, A.179, G.180, G.181 Chain D: G.412, G.413, V.438, M.439 Ligands: DXX.3 18 PLIP interactions: 12 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: A:P.177, D:V.438 Hydrogen bonds: A:S.110, A:G.140, A:A.142, A:I.144, A:A.179, A:G.181, D:G.413 Water bridges: A:R.34, A:Q.41, A:Q.145, A:A.182, D:Y.411, D:S.414, D:S.414, D:V.438 Salt bridges: A:R.34 MCA.6: 19 residues within 4Å: Chain B: R.34, F.104, M.107, G.108, S.110, G.140, G.141, A.142, R.143, I.144, Q.145, P.177, G.180, G.181 Chain E: G.412, G.413, V.438, M.439 Ligands: DXX.7 18 PLIP interactions: 14 interactions with chain B, 4 interactions with chain E Hydrophobic interactions: B:P.177, E:V.438 Hydrogen bonds: B:G.140, B:G.140, B:A.142, B:I.144, B:Q.145, B:G.181, E:G.413 Water bridges: B:R.34, B:K.37, B:K.37, B:K.37, B:A.179, B:A.182, E:S.414, E:R.450 Salt bridges: B:R.34 MCA.10: 22 residues within 4Å: Chain C: R.34, F.104, M.107, G.108, S.110, G.140, G.141, A.142, R.143, I.144, Q.145, P.177, A.179, G.180, G.181 Chain F: G.412, G.413, V.438, M.439, V.447, R.450 Ligands: DXX.11 18 PLIP interactions: 12 interactions with chain C, 6 interactions with chain F Hydrophobic interactions: C:P.177, F:V.438 Hydrogen bonds: C:S.110, C:G.140, C:A.142, C:I.144, C:Q.145, C:A.179, C:G.181, F:G.413, F:R.450, F:R.450 Water bridges: C:K.37, C:K.37, C:A.182, F:S.414 Salt bridges: C:R.34, F:R.450 MCA.12: 21 residues within 4Å: Chain A: G.412, G.413, V.438, M.439, K.451 Chain D: R.34, F.104, M.107, G.108, S.110, G.140, G.141, A.142, R.143, I.144, Q.145, P.177, G.180, G.181, Q.206 Ligands: DXX.13 24 PLIP interactions: 16 interactions with chain D, 8 interactions with chain A Hydrophobic interactions: D:P.177, A:V.438 Hydrogen bonds: D:S.110, D:G.140, D:G.140, D:A.142, D:I.144, D:G.181, D:Q.206, A:G.413 Water bridges: D:K.37, D:K.37, D:K.37, D:Q.41, D:Q.145, D:A.182, A:Y.411, A:Y.411, A:S.414, A:S.414, A:V.438 Salt bridges: D:R.34, D:K.37, A:K.451 MCA.14: 20 residues within 4Å: Chain B: G.412, G.413, V.438, M.439, R.450 Chain E: R.34, F.104, M.107, G.108, S.110, G.140, A.142, R.143, I.144, Q.145, P.177, A.179, G.180, G.181 Ligands: DXX.15 20 PLIP interactions: 13 interactions with chain E, 7 interactions with chain B Hydrophobic interactions: E:P.177, B:V.438 Hydrogen bonds: E:G.140, E:A.142, E:I.144, E:Q.145, E:A.179, E:G.181, B:G.413, B:R.450, B:R.450 Water bridges: E:K.37, E:K.37, E:Q.41, E:M.107, E:A.182, B:S.414, B:S.414 Salt bridges: E:R.34, B:R.450 MCA.16: 20 residues within 4Å: Chain C: G.412, G.413, V.438, M.439, V.447, R.450 Chain F: R.34, F.104, M.107, G.108, S.110, G.140, G.141, A.142, R.143, I.144, Q.145, P.177, G.180, G.181 22 PLIP interactions: 13 interactions with chain F, 9 interactions with chain C Hydrophobic interactions: F:P.177, C:V.438 Hydrogen bonds: F:G.140, F:G.140, F:A.142, F:I.144, F:Q.145, F:G.181, C:G.413 Water bridges: F:K.37, F:K.37, F:Q.41, F:Y.154, F:A.182, C:Y.411, C:S.414, C:V.438, C:R.450, C:K.451 Salt bridges: F:R.34, C:R.450, C:R.450 MCA.20: 20 residues within 4Å: Chain G: R.34, F.104, M.107, G.108, S.110, G.140, G.141, A.142, R.143, I.144, Q.145, P.177, A.179, G.180, G.181 Chain J: G.412, G.413, V.438, M.439 Ligands: DXX.21 19 PLIP interactions: 13 interactions with chain G, 6 interactions with chain J Hydrophobic interactions: G:P.177, J:V.438 Hydrogen bonds: G:S.110, G:G.140, G:A.142, G:I.144, G:A.179, G:G.181, J:G.413 Water bridges: G:R.34, G:Q.41, G:Q.145, G:Y.154, G:A.182, J:Y.411, J:S.414, J:S.414, J:V.438 Salt bridges: G:R.34 MCA.24: 19 residues within 4Å: Chain H: R.34, F.104, M.107, G.108, S.110, G.140, G.141, A.142, R.143, I.144, Q.145, P.177, G.180, G.181 Chain K: G.412, G.413, V.438, M.439 Ligands: DXX.25 18 PLIP interactions: 14 interactions with chain H, 4 interactions with chain K Hydrophobic interactions: H:P.177, K:V.438 Hydrogen bonds: H:G.140, H:G.140, H:A.142, H:I.144, H:Q.145, H:G.181, K:G.413 Water bridges: H:R.34, H:K.37, H:K.37, H:K.37, H:Y.154, H:A.182, K:S.414, K:R.450 Salt bridges: H:R.34 MCA.28: 22 residues within 4Å: Chain I: R.34, F.104, M.107, G.108, S.110, G.140, G.141, A.142, R.143, I.144, Q.145, P.177, A.179, G.180, G.181 Chain L: G.412, G.413, V.438, M.439, V.447, R.450 Ligands: DXX.29 18 PLIP interactions: 12 interactions with chain I, 6 interactions with chain L Hydrophobic interactions: I:P.177, L:V.438 Hydrogen bonds: I:S.110, I:G.140, I:A.142, I:I.144, I:Q.145, I:A.179, I:G.181, L:G.413, L:R.450, L:R.450 Water bridges: I:K.37, I:K.37, I:A.182, L:S.414 Salt bridges: I:R.34, L:R.450 MCA.30: 21 residues within 4Å: Chain G: G.412, G.413, V.438, M.439, K.451 Chain J: R.34, F.104, M.107, G.108, S.110, G.140, G.141, A.142, R.143, I.144, Q.145, P.177, G.180, G.181, Q.206 Ligands: DXX.31 24 PLIP interactions: 16 interactions with chain J, 8 interactions with chain G Hydrophobic interactions: J:P.177, G:V.438 Hydrogen bonds: J:S.110, J:G.140, J:G.140, J:A.142, J:I.144, J:G.181, J:Q.206, G:G.413 Water bridges: J:K.37, J:K.37, J:K.37, J:Q.41, J:Q.145, J:A.182, G:Y.411, G:Y.411, G:S.414, G:S.414, G:V.438 Salt bridges: J:R.34, J:K.37, G:K.451 MCA.32: 20 residues within 4Å: Chain H: G.412, G.413, V.438, M.439, R.450 Chain K: R.34, F.104, M.107, G.108, S.110, G.140, A.142, R.143, I.144, Q.145, P.177, A.179, G.180, G.181 Ligands: DXX.33 20 PLIP interactions: 13 interactions with chain K, 7 interactions with chain H Hydrophobic interactions: K:P.177, H:V.438 Hydrogen bonds: K:G.140, K:A.142, K:I.144, K:Q.145, K:A.179, K:G.181, H:G.413, H:R.450, H:R.450 Water bridges: K:K.37, K:K.37, K:Q.41, K:M.107, K:A.182, H:S.414, H:S.414 Salt bridges: K:R.34, H:R.450 MCA.34: 20 residues within 4Å: Chain I: G.412, G.413, V.438, M.439, V.447, R.450 Chain L: R.34, F.104, M.107, G.108, S.110, G.140, G.141, A.142, R.143, I.144, Q.145, P.177, G.180, G.181 21 PLIP interactions: 9 interactions with chain I, 12 interactions with chain L Hydrophobic interactions: I:V.438, L:P.177 Hydrogen bonds: I:G.413, L:G.140, L:G.140, L:A.142, L:I.144, L:Q.145, L:G.181 Water bridges: I:Y.411, I:S.414, I:V.438, I:R.450, I:K.451, L:K.37, L:K.37, L:Q.41, L:A.182 Salt bridges: I:R.450, I:R.450, L:R.34

12 x DXX: METHYLMALONIC ACID(Non-covalent)

DXX.3: 5 residues within 4Å: Chain A: T.203, G.204, V.207 Chain D: M.439 Ligands: MCA.2 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:T.203, A:V.207 Hydrogen bonds: A:G.204 Water bridges: D:G.440 DXX.7: 4 residues within 4Å: Chain B: T.203, G.204, V.207 Ligands: MCA.6 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: B:V.207 Hydrogen bonds: B:G.204 Water bridges: E:V.438 DXX.11: 4 residues within 4Å: Chain C: T.203, G.204, V.207 Ligands: MCA.10 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:V.207 Hydrogen bonds: C:G.204 Water bridges: C:G.181, F:V.438 DXX.13: 5 residues within 4Å: Chain D: I.202, T.203, G.204, V.207 Ligands: MCA.12 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.204 Water bridges: D:G.181, D:V.207 DXX.15: 7 residues within 4Å: Chain B: M.439 Chain E: G.180, I.202, T.203, G.204, V.207 Ligands: MCA.14 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.204 DXX.17: 5 residues within 4Å: Chain C: M.439 Chain F: I.202, T.203, G.204, V.207 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:T.203 Hydrogen bonds: F:G.204 DXX.21: 5 residues within 4Å: Chain G: T.203, G.204, V.207 Chain J: M.439 Ligands: MCA.20 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain J Hydrophobic interactions: G:T.203, G:V.207 Hydrogen bonds: G:G.204 Water bridges: J:G.440 DXX.25: 4 residues within 4Å: Chain H: T.203, G.204, V.207 Ligands: MCA.24 3 PLIP interactions: 1 interactions with chain K, 2 interactions with chain H Water bridges: K:V.438 Hydrophobic interactions: H:V.207 Hydrogen bonds: H:G.204 DXX.29: 4 residues within 4Å: Chain I: T.203, G.204, V.207 Ligands: MCA.28 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain L Hydrophobic interactions: I:V.207 Hydrogen bonds: I:G.204 Water bridges: I:G.181, L:V.438 DXX.31: 5 residues within 4Å: Chain J: I.202, T.203, G.204, V.207 Ligands: MCA.30 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:G.204 Water bridges: J:G.181, J:V.207 DXX.33: 7 residues within 4Å: Chain H: M.439 Chain K: G.180, I.202, T.203, G.204, V.207 Ligands: MCA.32 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:G.204 DXX.35: 5 residues within 4Å: Chain I: M.439 Chain L: I.202, T.203, G.204, V.207 2 PLIP interactions: 2 interactions with chain L Hydrophobic interactions: L:T.203 Hydrogen bonds: L:G.204

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

MPD.4: 4 residues within 4Å: Chain A: K.250, N.267, W.302, D.304 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.302 Hydrogen bonds: A:N.267, A:W.302 Water bridges: A:K.250 MPD.8: 5 residues within 4Å: Chain B: K.250, V.266, N.267, W.302, D.304 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:D.304 Hydrogen bonds: B:W.302 MPD.18: 5 residues within 4Å: Chain F: K.250, N.267, W.302, D.304 Chain L: L.246 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:W.302 Water bridges: F:W.302 MPD.22: 4 residues within 4Å: Chain G: K.250, N.267, W.302, D.304 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:W.302 Hydrogen bonds: G:N.267, G:W.302 Water bridges: G:K.250 MPD.26: 5 residues within 4Å: Chain H: K.250, V.266, N.267, W.302, D.304 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:D.304 Hydrogen bonds: H:W.302 MPD.36: 5 residues within 4Å: Chain F: L.246 Chain L: K.250, N.267, W.302, D.304 2 PLIP interactions: 2 interactions with chain L Hydrophobic interactions: L:W.302 Water bridges: L:W.302

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: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
A

H
B

I
C

J
D

K
E

L
F

Methylmalonyl-CoA carboxyltransferase 12S subunit

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