SMTL ID : 3vpb.1

ArgX from Sulfolobus tokodaii complexed with LysW/Glu/ADP/Mg/Zn/Sulfate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-4-2-mer

Ligands

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 25 residues within 4Å: Chain A: K.87, I.125, K.127, G.131, S.132, W.133, G.134, V.137, Q.167, E.168, Y.169, I.170, D.176, R.192, W.199, R.200, A.201, N.202, D.237, L.239, N.249, E.250 Ligands: MG.3, ZN.4, SO4.5 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:K.127, A:S.132, A:W.133, A:G.134, A:R.135, A:Q.167, A:I.170, A:A.201, A:N.202, A:N.202, A:N.249 Water bridges: A:K.87, A:K.87, A:Q.171, A:R.192, A:R.192, A:R.192, A:R.192 Salt bridges: A:K.87, A:K.87, A:K.127 ADP.6: 26 residues within 4Å: Chain B: K.87, I.125, K.127, G.131, S.132, W.133, G.134, R.135, V.137, Q.167, E.168, Y.169, I.170, D.176, R.192, W.199, R.200, A.201, N.202, D.237, L.239, N.249, E.250 Ligands: MG.8, ZN.9, SO4.10 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:K.127, B:S.132, B:W.133, B:G.134, B:R.135, B:Q.167, B:I.170, B:D.176, B:A.201, B:N.202, B:N.202, B:N.249 Water bridges: B:K.87, B:K.87, B:R.192, B:R.192, B:R.192, B:R.192 Salt bridges: B:K.87, B:K.87, B:K.127 ADP.11: 25 residues within 4Å: Chain C: K.87, I.125, K.127, G.131, S.132, W.133, G.134, R.135, V.137, Q.167, E.168, Y.169, I.170, D.176, R.192, W.199, R.200, A.201, N.202, D.237, L.239, N.249, E.250 Ligands: MG.13, SO4.14 25 PLIP interactions: 25 interactions with chain C Hydrogen bonds: C:K.127, C:S.132, C:W.133, C:G.134, C:R.135, C:Q.167, C:I.170, C:D.176, C:D.176, C:A.201, C:N.202, C:N.202, C:D.237, C:N.249 Water bridges: C:K.87, C:K.87, C:K.87, C:R.192, C:R.192, C:R.192, C:R.192, C:N.252 Salt bridges: C:K.87, C:K.87, C:K.127 ADP.16: 25 residues within 4Å: Chain D: K.87, I.125, K.127, G.131, S.132, W.133, G.134, R.135, V.137, Q.167, E.168, Y.169, I.170, D.176, R.192, W.199, R.200, A.201, N.202, D.237, L.239, N.249, E.250 Ligands: MG.18, SO4.19 24 PLIP interactions: 24 interactions with chain D Hydrogen bonds: D:K.127, D:S.132, D:W.133, D:G.134, D:R.135, D:Q.167, D:I.170, D:D.176, D:D.176, D:A.201, D:N.202, D:N.202, D:D.237, D:N.249 Water bridges: D:K.87, D:K.87, D:K.87, D:R.192, D:R.192, D:R.192, D:R.192 Salt bridges: D:K.87, D:K.87, D:K.127

4 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.2: 14 residues within 4Å: Chain A: W.133, R.178, Y.190, R.192, N.202, V.203, A.204, E.256, F.257, K.258, G.259, F.260 Chain E: E.56 Ligands: SO4.5 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:V.203, A:E.256 Hydrogen bonds: A:V.203, A:A.204, A:E.256, A:K.258, A:G.259, A:F.260, E:E.56 Water bridges: A:E.13, A:E.256 Salt bridges: A:R.192 GLU.7: 14 residues within 4Å: Chain B: W.133, R.178, Y.190, R.192, N.202, V.203, A.204, E.256, F.257, K.258, G.259, F.260 Chain F: E.56 Ligands: SO4.10 13 PLIP interactions: 10 interactions with chain B, 1 interactions with chain F, 2 Ligand-Ligand interactions Hydrophobic interactions: B:V.203, B:E.256 Hydrogen bonds: B:Y.190, B:V.203, B:A.204, B:E.256, B:K.258, B:G.259, B:F.260, F:E.56, E.7, E.7 Salt bridges: B:R.192 GLU.12: 13 residues within 4Å: Chain C: W.133, R.178, Y.190, R.192, N.202, V.203, A.204, E.256, F.257, K.258, G.259, F.260 Ligands: SO4.14 11 PLIP interactions: 9 interactions with chain C, 2 Ligand-Ligand interactions Hydrophobic interactions: C:E.256 Hydrogen bonds: C:Y.190, C:Y.190, C:V.203, C:A.204, C:G.259, C:F.260, E.12, E.12 Water bridges: C:R.178 Salt bridges: C:R.192 GLU.17: 13 residues within 4Å: Chain D: W.133, R.178, Y.190, R.192, N.202, V.203, A.204, E.256, F.257, K.258, G.259, F.260 Ligands: SO4.19 11 PLIP interactions: 11 interactions with chain D, Hydrophobic interactions: D:E.256 Hydrogen bonds: D:Y.190, D:V.203, D:A.204, D:E.256, D:K.258, D:G.259, D:F.260 Water bridges: D:R.178, D:R.178 Salt bridges: D:R.192

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: N.202, D.237, E.250 Ligands: ADP.1, ZN.4, SO4.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.237, A:E.250, H2O.2 MG.8: 6 residues within 4Å: Chain B: N.202, D.237, E.250 Ligands: ADP.6, ZN.9, SO4.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.237, B:E.250, H2O.12 MG.13: 4 residues within 4Å: Chain C: D.237, E.250 Ligands: ADP.11, SO4.14 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.237, C:E.250, H2O.23 MG.18: 5 residues within 4Å: Chain D: N.202, D.237, E.250 Ligands: ADP.16, SO4.19 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.237, D:E.250, H2O.32

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 7 residues within 4Å: Chain A: K.87, G.131, E.250, N.252 Ligands: ADP.1, MG.3, SO4.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.250, A:E.250, H2O.4 ZN.9: 5 residues within 4Å: Chain B: E.250, N.252 Ligands: ADP.6, MG.8, SO4.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.250, B:E.250, H2O.12 ZN.21: 4 residues within 4Å: Chain E: C.6, C.9, H.27, C.29 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.6, E:C.9, E:H.27, E:C.29 ZN.22: 4 residues within 4Å: Chain F: C.6, C.9, H.27, C.29 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.6, F:C.9, F:H.27, F:C.29

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

SO4.5: 13 residues within 4Å: Chain A: S.132, W.133, R.178, R.192, N.202, D.237, E.250, N.252 Chain E: E.56 Ligands: ADP.1, GLU.2, MG.3, ZN.4 9 PLIP interactions: 8 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:S.132, A:W.133, A:N.202, A:N.252, E.2 Water bridges: A:R.192, A:N.202 Salt bridges: A:R.178, A:R.192 SO4.10: 13 residues within 4Å: Chain B: S.132, W.133, R.178, R.192, N.202, D.237, E.250, N.252 Chain F: E.56 Ligands: ADP.6, GLU.7, MG.8, ZN.9 8 PLIP interactions: 7 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:S.132, B:W.133, B:R.192, B:N.202, E.7 Water bridges: B:R.192, B:N.202 Salt bridges: B:R.178 SO4.14: 11 residues within 4Å: Chain C: S.132, W.133, R.178, R.192, N.202, D.237, E.250, N.252 Ligands: ADP.11, GLU.12, MG.13 10 PLIP interactions: 8 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: C:W.133, C:N.202, C:N.252, C:N.252, E.12, E.12 Water bridges: C:R.178, C:R.192 Salt bridges: C:R.178, C:R.192 SO4.15: 4 residues within 4Å: Chain C: S.56, M.57, Y.58 Chain D: S.159 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.56, C:M.57, C:Y.58, D:S.159 SO4.19: 11 residues within 4Å: Chain D: S.132, W.133, R.178, R.192, N.202, D.237, E.250, N.252 Ligands: ADP.16, GLU.17, MG.18 11 PLIP interactions: 9 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: D:W.133, D:N.202, D:E.250, D:E.250, E.17, E.17 Water bridges: D:S.132, D:R.178, D:R.192 Salt bridges: D:R.178, D:R.192 SO4.20: 4 residues within 4Å: Chain C: S.159 Chain D: S.56, M.57, Y.58 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.56, D:M.57, D:Y.58, C:S.159, C:S.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ouchi, T. et al., Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus. Nat.Chem.Biol. (2013)

Release Date

2013-02-27

Peptides

Putative acetylornithine deacetylase: ABCD
Alpha-aminoadipate carrier protein lysW: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Putative acetylornithine deacetylase

Alpha-aminoadipate carrier protein lysW

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