SMTL ID : 4m9d.1

The Crystal structure of an adenylosuccinate synthetase from Bacillus anthracis str. Ames Ancestor in complex with AMP.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 18 residues within 4Å: Chain A: W.14, G.15, N.41, A.42, I.128, G.129, T.130, T.131, Q.226, L.230, V.240, T.241, R.274, V.275, G.276 Chain B: R.145 Ligands: EDO.3, EDO.4 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.41, A:N.41, A:I.128, A:G.129, A:T.131, A:Q.226, A:T.241, A:R.274, A:G.276 Water bridges: A:K.19, A:T.130, A:K.132, A:I.135, A:G.136, A:Q.226, A:S.242, A:V.275, A:V.275, A:D.277 Salt bridges: B:R.145 AMP.6: 17 residues within 4Å: Chain A: R.145 Chain B: W.14, G.15, D.16, N.41, A.42, G.129, T.130, T.131, Q.226, L.230, V.240, T.241, V.275, G.276 Ligands: MLI.8, FMT.13 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.41, B:N.41, B:G.129, B:T.131, B:Q.226, B:R.274, B:G.276 Water bridges: B:D.16, B:G.43, B:I.128, B:T.131, B:K.132, B:G.136, B:G.136, B:T.241, B:S.242, B:V.275, B:V.275, B:D.277 Salt bridges: A:R.145

3 x MLI: MALONATE ION(Non-functional Binders)

MLI.2: 9 residues within 4Å: Chain A: G.15, D.16, E.17, G.18, K.19, G.20, G.43, H.44 Ligands: EDO.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:D.16, A:D.16, A:E.17, A:E.17, A:G.18, A:K.19, A:G.20 Water bridges: A:G.18, A:K.21, A:G.43 Salt bridges: A:K.19, A:K.19, A:H.44, A:K.269 MLI.7: 7 residues within 4Å: Chain A: V.264, G.325, T.327 Chain B: G.257, P.258, A.259, K.260 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.259 Hydrogen bonds: B:A.259, B:K.260 MLI.8: 5 residues within 4Å: Chain B: N.41, T.131, K.133 Ligands: AMP.6, EDO.11 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:T.131 Water bridges: B:R.307, B:R.307, B:R.307 Salt bridges: B:K.133

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: G.15, D.16, G.43, R.307 Ligands: AMP.1, MLI.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.16, A:D.16 Water bridges: A:G.15, A:K.19, A:G.43, A:G.43 EDO.4: 4 residues within 4Å: Chain A: N.41, T.131, K.133 Ligands: AMP.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.133 EDO.9: 5 residues within 4Å: Chain A: D.215, K.260 Chain B: R.321, G.325, L.326 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.215, A:K.260, B:L.326 EDO.10: 3 residues within 4Å: Chain B: Q.201, V.203, C.204 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.203 EDO.11: 5 residues within 4Å: Chain B: G.300, T.301, T.302, T.303 Ligands: MLI.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.302, B:T.303, B:T.303 Water bridges: B:T.301 EDO.12: 2 residues within 4Å: Chain B: E.28, H.29 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.28

3 x FMT: FORMIC ACID(Non-functional Binders)

FMT.5: 5 residues within 4Å: Chain A: E.358, P.360, A.361, N.362 Chain B: N.103 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.358, A:A.361, A:N.362 Water bridges: B:N.103, B:R.104 FMT.13: 7 residues within 4Å: Chain B: K.19, A.42, G.43, A.225, Q.226 Ligands: AMP.6, PO4.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.19, B:G.43, B:G.43, B:Q.226 FMT.14: 4 residues within 4Å: Chain B: G.129, V.275, G.276, D.277 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.129, B:T.130

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.15: 8 residues within 4Å: Chain B: D.16, E.17, G.18, K.19, G.20, G.43, H.44 Ligands: FMT.13 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:D.16, B:E.17, B:G.18, B:K.19, B:G.20, B:G.43 Water bridges: B:K.19, B:K.19, B:K.21, B:G.43 Salt bridges: B:K.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, K. et al., The Crystal structure of an adenylosuccinate synthetase from Bacillus anthracis str. Ames Ancestor in complex with AMP. To be Published

Release Date

2013-08-28

Peptides

Adenylosuccinate synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Adenylosuccinate synthetase

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