SMTL ID : 5ls7.1

Complex of wild type E. coli alpha aspartate decarboxylase with its processing factor PanZ

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.16 Å

Oligo State

hetero-4-4-4-mer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain B: D.99, R.105, T.109, A.119, Q.120, G.122, G.123, W.124 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.109, B:Q.120, B:G.122 GOL.7: 8 residues within 4Å: Chain C: Q.6, L.9, D.10, G.13, I.14, L.15, E.16 Chain I: R.75 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain I Hydrogen bonds: C:Q.6, C:E.16, I:R.75, I:R.75 GOL.13: 8 residues within 4Å: Chain E: D.99, R.105, T.109, A.119, Q.120, G.122, G.123, W.124 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.109, E:Q.120, E:G.122 GOL.19: 8 residues within 4Å: Chain F: Q.6, L.9, D.10, G.13, I.14, L.15, E.16 Chain L: R.75 4 PLIP interactions: 2 interactions with chain L, 2 interactions with chain F Hydrogen bonds: L:R.75, L:R.75, F:Q.6, F:E.16 GOL.25: 8 residues within 4Å: Chain H: D.99, R.105, T.109, A.119, Q.120, G.122, G.123, W.124 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:T.109, H:Q.120, H:G.122 GOL.31: 8 residues within 4Å: Chain F: R.75 Chain I: Q.6, L.9, D.10, G.13, I.14, L.15, E.16 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain F Hydrogen bonds: I:Q.6, I:E.16, F:R.75, F:R.75 GOL.37: 8 residues within 4Å: Chain K: D.99, R.105, T.109, A.119, Q.120, G.122, G.123, W.124 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:T.109, K:Q.120, K:G.122 GOL.43: 8 residues within 4Å: Chain C: R.75 Chain L: Q.6, L.9, D.10, G.13, I.14, L.15, E.16 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain L Hydrogen bonds: C:R.75, C:R.75, L:Q.6, L:E.16

8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 5 residues within 4Å: Chain B: I.5, R.7, Y.40, E.84, N.88 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.84 PEG.10: 6 residues within 4Å: Chain A: I.19 Chain C: T.68 Chain G: I.19 Ligands: PEG.22, PEG.34, PEG.46 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.68 Water bridges: C:T.68 PEG.14: 5 residues within 4Å: Chain E: I.5, R.7, Y.40, E.84, N.88 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.84 PEG.22: 6 residues within 4Å: Chain D: I.19 Chain F: T.68 Chain J: I.19 Ligands: PEG.10, PEG.34, PEG.46 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:T.68 Water bridges: F:T.68 PEG.26: 5 residues within 4Å: Chain H: I.5, R.7, Y.40, E.84, N.88 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:E.84 PEG.34: 6 residues within 4Å: Chain D: I.19 Chain G: I.19 Chain I: T.68 Ligands: PEG.10, PEG.22, PEG.46 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:T.68 Water bridges: I:T.68 PEG.38: 5 residues within 4Å: Chain K: I.5, R.7, Y.40, E.84, N.88 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:E.84 PEG.46: 6 residues within 4Å: Chain A: I.19 Chain J: I.19 Chain L: T.68 Ligands: PEG.10, PEG.22, PEG.34 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:T.68 Water bridges: L:T.68

4 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.3: 24 residues within 4Å: Chain B: W.23, E.25, Y.26, S.65, L.66, R.67, V.68, R.73, R.74, R.75, G.76, V.77, G.78, Q.79, G.101, V.102, E.103, V.107, M.108, A.110, F.111, A.114 Chain C: R.78 Ligands: MG.4 30 PLIP interactions: 27 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:Y.26, B:L.66, B:V.68 Hydrogen bonds: B:L.66, B:V.68, B:R.73, B:R.74, B:R.74, B:R.75, B:G.76, B:G.76, B:V.77, B:G.78, B:Q.79, B:E.103 Water bridges: B:R.67, B:R.67, B:R.74, B:R.74, B:Q.79, B:E.103, B:D.104, B:A.110, B:A.114, C:R.78, C:R.78 Salt bridges: B:R.74, C:R.78 pi-Cation interactions: B:R.74, B:R.74 ACO.15: 24 residues within 4Å: Chain E: W.23, E.25, Y.26, S.65, L.66, R.67, V.68, R.73, R.74, R.75, G.76, V.77, G.78, Q.79, G.101, V.102, E.103, V.107, M.108, A.110, F.111, A.114 Chain F: R.78 Ligands: MG.16 30 PLIP interactions: 27 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: E:Y.26, E:L.66, E:V.68 Hydrogen bonds: E:L.66, E:V.68, E:R.73, E:R.74, E:R.74, E:R.75, E:G.76, E:G.76, E:V.77, E:G.78, E:Q.79, E:E.103 Water bridges: E:R.67, E:R.67, E:R.74, E:R.74, E:Q.79, E:E.103, E:D.104, E:A.110, E:A.114, F:R.78, F:R.78 Salt bridges: E:R.74, F:R.78 pi-Cation interactions: E:R.74, E:R.74 ACO.27: 24 residues within 4Å: Chain H: W.23, E.25, Y.26, S.65, L.66, R.67, V.68, R.73, R.74, R.75, G.76, V.77, G.78, Q.79, G.101, V.102, E.103, V.107, M.108, A.110, F.111, A.114 Chain I: R.78 Ligands: MG.28 30 PLIP interactions: 27 interactions with chain H, 3 interactions with chain I Hydrophobic interactions: H:Y.26, H:L.66, H:V.68 Hydrogen bonds: H:L.66, H:V.68, H:R.73, H:R.74, H:R.74, H:R.75, H:G.76, H:G.76, H:V.77, H:G.78, H:Q.79, H:E.103 Water bridges: H:R.67, H:R.67, H:R.74, H:R.74, H:Q.79, H:E.103, H:D.104, H:A.110, H:A.114, I:R.78, I:R.78 Salt bridges: H:R.74, I:R.78 pi-Cation interactions: H:R.74, H:R.74 ACO.39: 24 residues within 4Å: Chain K: W.23, E.25, Y.26, S.65, L.66, R.67, V.68, R.73, R.74, R.75, G.76, V.77, G.78, Q.79, G.101, V.102, E.103, V.107, M.108, A.110, F.111, A.114 Chain L: R.78 Ligands: MG.40 30 PLIP interactions: 27 interactions with chain K, 3 interactions with chain L Hydrophobic interactions: K:Y.26, K:L.66, K:V.68 Hydrogen bonds: K:L.66, K:V.68, K:R.73, K:R.74, K:R.74, K:R.75, K:G.76, K:G.76, K:V.77, K:G.78, K:Q.79, K:E.103 Water bridges: K:R.67, K:R.67, K:R.74, K:R.74, K:Q.79, K:E.103, K:D.104, K:A.110, K:A.114, L:R.78, L:R.78 Salt bridges: K:R.74, L:R.78 pi-Cation interactions: K:R.74, K:R.74

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 7 residues within 4Å: Chain B: T.72, R.73, R.74, R.75, G.76, V.77 Ligands: ACO.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.72 MG.16: 7 residues within 4Å: Chain E: T.72, R.73, R.74, R.75, G.76, V.77 Ligands: ACO.15 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.72 MG.28: 7 residues within 4Å: Chain H: T.72, R.73, R.74, R.75, G.76, V.77 Ligands: ACO.27 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.72 MG.40: 7 residues within 4Å: Chain K: T.72, R.73, R.74, R.75, G.76, V.77 Ligands: ACO.39 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:T.72

12 x CO2: CARBON DIOXIDE(Non-covalent)

CO2.5: 4 residues within 4Å: Chain B: K.21, R.69, E.70, R.73 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.70 Water bridges: B:V.71 CO2.6: 1 residues within 4Å: Chain B: E.70 No protein-ligand interaction detected (PLIP) CO2.12: 3 residues within 4Å: Chain C: G.86, D.87, E.89 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.87 CO2.17: 4 residues within 4Å: Chain E: K.21, R.69, E.70, R.73 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.70 Water bridges: E:V.71 CO2.18: 1 residues within 4Å: Chain E: E.70 No protein-ligand interaction detected (PLIP) CO2.24: 3 residues within 4Å: Chain F: G.86, D.87, E.89 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.87 CO2.29: 4 residues within 4Å: Chain H: K.21, R.69, E.70, R.73 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:E.70 Water bridges: H:V.71 CO2.30: 1 residues within 4Å: Chain H: E.70 No protein-ligand interaction detected (PLIP) CO2.36: 3 residues within 4Å: Chain I: G.86, D.87, E.89 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:D.87 CO2.41: 4 residues within 4Å: Chain K: K.21, R.69, E.70, R.73 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:E.70 Water bridges: K:V.71 CO2.42: 1 residues within 4Å: Chain K: E.70 No protein-ligand interaction detected (PLIP) CO2.48: 3 residues within 4Å: Chain L: G.86, D.87, E.89 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:D.87

8 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.8: 8 residues within 4Å: Chain A: G.41 Chain C: X.1, N.48, A.50, A.51 Chain I: W.23, R.30, I.62 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain I Hydrogen bonds: C:A.50, C:A.51, I:R.30, I:R.30 SCN.9: 7 residues within 4Å: Chain B: N.45, R.47 Chain C: Q.100, V.101 Chain J: H.34, Y.39 Chain L: I.44 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain J Water bridges: C:A.102 Hydrogen bonds: J:Y.39 SCN.20: 8 residues within 4Å: Chain D: G.41 Chain F: X.1, N.48, A.50, A.51 Chain L: W.23, R.30, I.62 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain L Hydrogen bonds: F:A.50, F:A.51, L:R.30, L:R.30 SCN.21: 7 residues within 4Å: Chain E: N.45, R.47 Chain F: Q.100, V.101 Chain G: H.34, Y.39 Chain I: I.44 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:Y.39 Water bridges: F:A.102 SCN.32: 8 residues within 4Å: Chain F: W.23, R.30, I.62 Chain G: G.41 Chain I: X.1, N.48, A.50, A.51 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain F Hydrogen bonds: I:A.50, I:A.51, F:R.30, F:R.30 SCN.33: 7 residues within 4Å: Chain A: H.34, Y.39 Chain C: I.44 Chain H: N.45, R.47 Chain I: Q.100, V.101 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain A Water bridges: I:A.102 Hydrogen bonds: A:Y.39 SCN.44: 8 residues within 4Å: Chain C: W.23, R.30, I.62 Chain J: G.41 Chain L: X.1, N.48, A.50, A.51 4 PLIP interactions: 2 interactions with chain L, 2 interactions with chain C Hydrogen bonds: L:A.50, L:A.51, C:R.30, C:R.30 SCN.45: 7 residues within 4Å: Chain D: H.34, Y.39 Chain F: I.44 Chain K: N.45, R.47 Chain L: Q.100, V.101 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain D Water bridges: L:A.102 Hydrogen bonds: D:Y.39

4 x 74C: methyl radical(Covalent)

74C.11: 3 residues within 4Å: Chain C: D.7, F.8, M.90 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:D.7, C:F.8 74C.23: 3 residues within 4Å: Chain F: D.7, F.8, M.90 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:D.7, F:F.8 74C.35: 3 residues within 4Å: Chain I: D.7, F.8, M.90 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:D.7, I:F.8 74C.47: 3 residues within 4Å: Chain L: D.7, F.8, M.90 2 PLIP interactions: 2 interactions with chain L Hydrophobic interactions: L:D.7, L:F.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arnott, Z.L.P. et al., The Mechanism of Regulation of Pantothenate Biosynthesis by the PanD-PanZAcCoA Complex Reveals an Additional Mode of Action for the Antimetabolite N-Pentyl Pantothenamide (N5-Pan). Biochemistry (2017)

Release Date

2017-09-13

Peptides

Aspartate 1-decarboxylase: ADGJ
PanD maturation factor: BEHK
Aspartate 1-decarboxylase: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

J
A

B
B

E
B

H
B

K
B

C
D

F
D

I
D

L
D

Aspartate 1-decarboxylase

PanD maturation factor

Aspartate 1-decarboxylase

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