SMTL ID : 3etc.1 (2 other biounits)

2.1 A structure of acyl-adenylate synthetase from Methanosarcina acetivorans containing a link between Lys256 and Cys298

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x FOR: FORMYL GROUP(Covalent)

FOR.1: 5 residues within 4Å: Chain A: W.260, Q.261, T.271, K.279, C.321 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.261 FOR.13: 5 residues within 4Å: Chain B: W.260, Q.261, T.271, K.279, C.321 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.261, B:T.271

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 4 residues within 4Å: Chain A: D.80, N.307, E.310, K.311 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.310, A:K.311 PGE.14: 4 residues within 4Å: Chain B: D.80, N.307, E.310, K.311 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.80, B:K.311 PGE.15: 8 residues within 4Å: Chain B: K.279, W.282, F.373, G.374, Q.375, T.376 Ligands: GOL.20, GOL.21 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.376 Water bridges: B:K.279, B:G.350, B:Q.375

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.3: 14 residues within 4Å: Chain A: W.277, K.279, W.282, A.349, G.350, F.373, G.374, T.376, K.479, G.482, Y.483, K.484, Y.548 Ligands: GOL.12 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.376, A:T.376, A:K.479, A:K.479, A:K.484, A:Y.548, A:Y.548 Water bridges: A:S.234, A:K.279, A:G.350 1PE.4: 6 residues within 4Å: Chain A: N.535, Q.538, D.539, K.542, P.547, Y.550 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.535, A:K.542

3 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.5: 11 residues within 4Å: Chain A: S.120, Y.270, T.271, V.272, A.273, D.274, K.284, V.297, Y.298, Y.300, D.301 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.273, A:Y.298, A:Y.298 Water bridges: A:D.274 Salt bridges: A:D.274, A:K.284 EPE.6: 9 residues within 4Å: Chain A: V.436, W.449, H.450, D.451, G.452, Y.453 Chain B: E.155, E.180, C.181 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.426, A:D.451, A:G.452, A:Y.453, B:C.181 EPE.16: 11 residues within 4Å: Chain B: S.120, Y.270, T.271, V.272, A.273, D.274, K.284, V.297, Y.298, Y.300, D.301 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.270, B:A.273, B:Y.298, B:Y.298 Water bridges: B:K.284, B:Y.300 Salt bridges: B:D.274, B:K.284

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Chain B: D.112 No protein-ligand interaction detected (PLIP)

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.8: 9 residues within 4Å: Chain A: R.148, D.149, Y.152, R.153, F.239, P.240, E.489, T.545, K.549 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.148, A:R.148, A:D.149, A:R.153, A:R.153, A:E.489, A:T.545, A:K.549 NO3.18: 9 residues within 4Å: Chain B: R.148, D.149, Y.152, R.153, F.239, P.240, E.489, T.545, K.549 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.148, B:R.153, B:R.153, B:E.489, B:K.549

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 8 residues within 4Å: Chain A: K.48, I.49, L.255, P.400, G.401, Y.402, P.431, V.432 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.49, A:V.432 Water bridges: A:G.401 GOL.10: 7 residues within 4Å: Chain A: E.351, P.352, E.371, F.373, I.395, F.470, K.479 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.479 Water bridges: A:G.350, A:E.371, A:G.393 GOL.11: 9 residues within 4Å: Chain A: S.233, S.234, G.235, K.241, E.377, Y.438, R.444, I.477, K.484 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.377, A:R.444, A:R.444, A:K.484 Water bridges: A:S.233, A:K.241, A:Q.375, A:Y.438, A:R.444, A:D.475 GOL.12: 7 residues within 4Å: Chain A: Y.231, F.232, G.276, W.277, G.278, T.376 Ligands: 1PE.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.232, A:G.278 Water bridges: A:K.279, A:K.279 GOL.19: 9 residues within 4Å: Chain B: S.233, S.234, G.235, K.241, E.377, Y.438, R.444, I.477, K.484 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.233, B:R.444, B:R.444, B:K.484 Water bridges: B:S.233, B:K.241, B:Y.438, B:R.444, B:D.475 GOL.20: 8 residues within 4Å: Chain B: G.350, E.351, P.352, E.371, F.373, I.395, F.470 Ligands: PGE.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.350, B:G.393 GOL.21: 7 residues within 4Å: Chain B: G.374, Q.375, D.458, F.470, R.473, K.484 Ligands: PGE.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.374, B:Q.375, B:K.484

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shah, M.B. et al., The 2.1 A crystal structure of an acyl-CoA synthetase from Methanosarcina acetivorans reveals an alternate acyl-binding pocket for small branched acyl substrates. Proteins (2009)

Release Date

2009-07-07

Peptides

AMP-binding protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

AMP-binding protein

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