SMTL ID : 4ekn.2 (1 other biounit)

Structure of the catalytic chain of Methanococcus jannaschii Aspartate Transcarbamoylase in a hexagonal crystal form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

24 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 8 residues within 4Å: Chain A: K.63, V.69 Chain B: K.63, V.69 Chain C: K.63, V.69 Ligands: SO4.7, SO4.13 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain A: G.11, K.12, E.13 Ligand excluded by PLIP SO4.3: 1 residues within 4Å: Chain A: R.144 Ligand excluded by PLIP SO4.4: 6 residues within 4Å: Chain A: S.128, Y.162, G.163, R.164, T.165, R.226 Ligand excluded by PLIP SO4.7: 8 residues within 4Å: Chain A: K.63, V.69 Chain B: K.63, V.69 Chain C: K.63, V.69 Ligands: SO4.1, SO4.13 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain B: G.11, K.12, E.13 Ligand excluded by PLIP SO4.9: 1 residues within 4Å: Chain B: R.144 Ligand excluded by PLIP SO4.10: 6 residues within 4Å: Chain B: S.128, Y.162, G.163, R.164, T.165, R.226 Ligand excluded by PLIP SO4.13: 8 residues within 4Å: Chain A: K.63, V.69 Chain B: K.63, V.69 Chain C: K.63, V.69 Ligands: SO4.1, SO4.7 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain C: G.11, K.12, E.13 Ligand excluded by PLIP SO4.15: 1 residues within 4Å: Chain C: R.144 Ligand excluded by PLIP SO4.16: 6 residues within 4Å: Chain C: S.128, Y.162, G.163, R.164, T.165, R.226 Ligand excluded by PLIP SO4.19: 8 residues within 4Å: Chain D: K.63, V.69 Chain E: K.63, V.69 Chain F: K.63, V.69 Ligands: SO4.25, SO4.31 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain D: G.11, K.12, E.13 Ligand excluded by PLIP SO4.21: 1 residues within 4Å: Chain D: R.144 Ligand excluded by PLIP SO4.22: 6 residues within 4Å: Chain D: S.128, Y.162, G.163, R.164, T.165, R.226 Ligand excluded by PLIP SO4.25: 8 residues within 4Å: Chain D: K.63, V.69 Chain E: K.63, V.69 Chain F: K.63, V.69 Ligands: SO4.19, SO4.31 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain E: G.11, K.12, E.13 Ligand excluded by PLIP SO4.27: 1 residues within 4Å: Chain E: R.144 Ligand excluded by PLIP SO4.28: 6 residues within 4Å: Chain E: S.128, Y.162, G.163, R.164, T.165, R.226 Ligand excluded by PLIP SO4.31: 8 residues within 4Å: Chain D: K.63, V.69 Chain E: K.63, V.69 Chain F: K.63, V.69 Ligands: SO4.19, SO4.25 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain F: G.11, K.12, E.13 Ligand excluded by PLIP SO4.33: 1 residues within 4Å: Chain F: R.144 Ligand excluded by PLIP SO4.34: 6 residues within 4Å: Chain F: S.128, Y.162, G.163, R.164, T.165, R.226 Ligand excluded by PLIP

6 x K: POTASSIUM ION(Non-covalent)

K.5: 5 residues within 4Å: Chain A: E.68 Chain B: E.68 Chain C: E.68 Ligands: K.11, K.17 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 2 interactions with chain A Metal complexes: B:E.68, B:E.68, C:E.68, A:E.68, A:E.68 K.11: 5 residues within 4Å: Chain A: E.68 Chain B: E.68 Chain C: E.68 Ligands: K.5, K.17 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 2 interactions with chain A Metal complexes: B:E.68, B:E.68, C:E.68, A:E.68, A:E.68 K.17: 5 residues within 4Å: Chain A: E.68 Chain B: E.68 Chain C: E.68 Ligands: K.5, K.11 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 2 interactions with chain A Metal complexes: B:E.68, B:E.68, C:E.68, A:E.68, A:E.68 K.23: 5 residues within 4Å: Chain D: E.68 Chain E: E.68 Chain F: E.68 Ligands: K.29, K.35 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D, 2 interactions with chain F Metal complexes: E:E.68, E:E.68, D:E.68, F:E.68, F:E.68 K.29: 5 residues within 4Å: Chain D: E.68 Chain E: E.68 Chain F: E.68 Ligands: K.23, K.35 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D, 2 interactions with chain F Metal complexes: E:E.68, E:E.68, D:E.68, F:E.68, F:E.68 K.35: 5 residues within 4Å: Chain D: E.68 Chain E: E.68 Chain F: E.68 Ligands: K.23, K.29 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D, 2 interactions with chain F Metal complexes: E:E.68, E:E.68, D:E.68, F:E.68, F:E.68

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: K.36 Chain B: K.36 Ligands: GOL.12, GOL.18 9 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B, 3 interactions with chain A Water bridges: C:K.36, C:K.36, C:E.39, B:K.36, B:K.36, B:K.36, A:K.36, A:K.36, A:K.36 GOL.12: 4 residues within 4Å: Chain B: K.36 Chain C: K.36 Ligands: GOL.6, GOL.18 9 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A, 3 interactions with chain B Water bridges: C:K.36, C:K.36, C:K.36, A:K.36, A:E.39, A:E.39, B:K.36, B:K.36, B:K.36 GOL.18: 4 residues within 4Å: Chain A: K.36 Chain C: K.36 Ligands: GOL.6, GOL.12 9 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B, 3 interactions with chain A Water bridges: C:K.36, C:K.36, C:K.36, B:K.36, B:K.36, B:E.39, A:K.36, A:K.36, A:K.36 GOL.24: 4 residues within 4Å: Chain D: K.36 Chain E: K.36 Ligands: GOL.30, GOL.36 9 PLIP interactions: 3 interactions with chain F, 3 interactions with chain D, 3 interactions with chain E Water bridges: F:K.36, F:K.36, F:E.39, D:K.36, D:K.36, D:K.36, E:K.36, E:K.36, E:K.36 GOL.30: 4 residues within 4Å: Chain E: K.36 Chain F: K.36 Ligands: GOL.24, GOL.36 9 PLIP interactions: 3 interactions with chain D, 3 interactions with chain F, 3 interactions with chain E Water bridges: D:K.36, D:E.39, D:E.39, F:K.36, F:K.36, F:K.36, E:K.36, E:K.36, E:K.36 GOL.36: 4 residues within 4Å: Chain D: K.36 Chain F: K.36 Ligands: GOL.24, GOL.30 9 PLIP interactions: 3 interactions with chain F, 3 interactions with chain D, 3 interactions with chain E Water bridges: F:K.36, F:K.36, F:K.36, D:K.36, D:K.36, D:K.36, E:K.36, E:K.36, E:E.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vitali, J. et al., Structure of the catalytic chain of Methanococcus jannaschii aspartate transcarbamoylase in a hexagonal crystal form: insights into the path of carbamoyl phosphate to the active site of the enzyme. Acta Crystallogr.,Sect.F (2012)

Release Date

2012-05-09

Peptides

Aspartate carbamoyltransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

D
B

E
B

F
B

Aspartate carbamoyltransferase

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