SMTL ID : 4r1l.3 (2 other biounits)

Crystal structure of a Putative Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.42 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.252, H.259, C.314, C.316 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.252, A:H.259, A:C.314, A:C.316 ZN.16: 4 residues within 4Å: Chain B: C.252, H.259, C.314, C.316 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.252, B:H.259, B:C.314, B:C.316 ZN.22: 4 residues within 4Å: Chain C: C.252, H.259, C.314, C.316 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.252, C:H.259, C:C.314, C:C.316 ZN.32: 4 residues within 4Å: Chain D: C.252, H.259, C.314, C.316 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.252, D:H.259, D:C.314, D:C.316

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

ADP.2: 19 residues within 4Å: Chain A: G.214, A.215, E.216, P.217, N.236, S.237, F.238, G.239, M.240, T.241, D.305, I.326, R.329, I.335, G.338, N.340 Ligands: AMP.3, K.5, PGE.8 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:A.215, A:S.237, A:G.239, A:T.241, A:T.241, A:T.241, A:D.305, A:R.329, A:N.340 Water bridges: A:T.143, A:G.144, A:I.326 ADP.17: 17 residues within 4Å: Chain B: S.94, T.143, G.214, A.215, E.216, P.217, N.236, S.237, F.238, G.239, M.240, T.241, D.305, I.326, R.329, K.425 Ligands: EDO.20 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:A.215, B:S.237, B:G.239, B:T.241, B:T.241, B:D.305, B:R.329, B:K.425 Water bridges: B:S.137, B:T.143, B:T.143, B:G.144, B:N.236, B:N.236 Salt bridges: B:K.425, B:K.425 ADP.33: 16 residues within 4Å: Chain D: T.143, G.214, A.215, E.216, P.217, N.236, S.237, F.238, G.239, M.240, T.241, D.305, I.326, R.329, K.425 Ligands: PEG.35 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:A.215, D:S.237, D:G.239, D:T.241, D:T.241, D:D.305, D:R.329, D:K.425 Water bridges: D:N.236, D:G.239, D:I.326 Salt bridges: D:K.425, D:K.425

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 17 residues within 4Å: Chain A: A.215, E.216, P.217, N.236, S.237, F.238, G.239, M.240, T.241, D.305, I.326, R.329, I.335, N.340 Ligands: ADP.2, K.5, PGE.8 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:T.143, A:A.215, A:S.237, A:G.239, A:T.241, A:T.241, A:T.241, A:D.305, A:R.329, A:N.340 Water bridges: A:N.236, A:I.326 AMP.23: 16 residues within 4Å: Chain C: G.214, A.215, E.216, P.217, N.236, S.237, F.238, G.239, M.240, T.241, D.305, I.326, R.329, I.335, N.340 Ligands: K.25 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:A.215, C:S.237, C:G.239, C:T.241, C:D.305, C:R.329 Water bridges: C:T.143, C:N.236, C:T.241, C:T.241, C:T.241, C:T.303

2 x COA: COENZYME A(Non-covalent)

COA.4: 12 residues within 4Å: Chain A: S.136, A.164, G.165, N.166, S.167, I.185, Y.188, R.191, K.337, V.407, T.408 Ligands: SO4.9 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.165, A:N.166, A:S.167, A:K.337, A:Q.370, A:T.408, A:T.408, A:T.408 Water bridges: A:N.166 Salt bridges: A:R.191, A:K.337, A:K.337 pi-Stacking: A:Y.188 COA.24: 12 residues within 4Å: Chain C: S.136, A.164, G.165, N.166, S.167, I.185, Y.188, R.191, K.337, V.407, T.408 Ligands: SO4.27 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:G.165, C:N.166, C:S.167, C:S.167, C:K.337, C:Q.370, C:T.408, C:T.408 Water bridges: C:I.185, C:T.408, C:T.408 Salt bridges: C:R.191, C:K.337, C:K.337, C:K.402 pi-Stacking: C:Y.188

6 x K: POTASSIUM ION(Non-covalent)

K.5: 6 residues within 4Å: Chain A: A.215, I.335, G.338, N.340 Ligands: ADP.2, AMP.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:A.215, A:G.338 K.6: 7 residues within 4Å: Chain A: M.84, K.85, G.88 Chain B: K.129, G.156, C.157, L.158 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:K.85, A:G.88, B:K.129, B:G.156, H2O.7 K.7: 7 residues within 4Å: Chain A: K.129, G.156, C.157, L.158 Chain B: M.84, K.85, G.88 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:K.129, A:G.156, B:K.85, B:G.88 K.25: 5 residues within 4Å: Chain C: A.215, I.335, G.338, N.340 Ligands: AMP.23 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:A.215, C:G.338 K.26: 8 residues within 4Å: Chain C: M.84, K.85, R.86, G.88 Chain D: K.129, G.156, C.157, L.158 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:K.85, C:G.88, D:K.129, D:G.156, H2O.12 K.34: 7 residues within 4Å: Chain C: K.129, G.156, C.157, L.158 Chain D: M.84, K.85, G.88 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:K.85, D:G.88, C:K.129, C:G.156, H2O.22

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

PGE.8: 14 residues within 4Å: Chain A: S.137, G.138, F.142, G.144, H.183, I.185, A.215, G.239, P.246, K.337, G.338, V.339 Ligands: ADP.2, AMP.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.138, A:G.239 Water bridges: A:S.137

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

SO4.9: 5 residues within 4Å: Chain A: N.166, S.167, Y.188, R.191 Ligands: COA.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.166, A:S.167, A:S.167, A:Y.188 Water bridges: A:K.168 Salt bridges: A:R.191 SO4.10: 4 residues within 4Å: Chain A: G.48, D.52, S.53, K.62 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.52 Water bridges: A:K.62 Salt bridges: A:K.62 SO4.11: 4 residues within 4Å: Chain A: R.394, R.395 Chain D: R.394, R.395 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Water bridges: D:R.395 Salt bridges: D:R.394, D:R.395, A:R.394, A:R.395 SO4.18: 4 residues within 4Å: Chain B: N.166, S.167, Y.188, R.191 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Water bridges: A:D.403, B:N.166 Hydrogen bonds: B:N.166, B:S.167, B:S.167, B:Y.188 Salt bridges: B:R.191 SO4.27: 5 residues within 4Å: Chain C: N.166, S.167, Y.188, R.191 Ligands: COA.24 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.166, C:S.167 Salt bridges: C:R.191 SO4.28: 3 residues within 4Å: Chain B: R.394 Chain C: R.394, R.395 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Water bridges: B:R.394, B:R.394 Salt bridges: B:R.394, C:R.394, C:R.395, C:K.410 SO4.36: 5 residues within 4Å: Chain D: G.165, N.166, S.167, Y.188, R.191 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.166, D:S.167, D:S.167, D:S.167 Water bridges: D:K.168 Salt bridges: D:R.191

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

EDO.12: 7 residues within 4Å: Chain A: I.31, N.32, A.35, F.44, I.49, T.50, G.51 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.32, A:I.49 EDO.13: 1 residues within 4Å: Chain A: K.46 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.46 EDO.14: 8 residues within 4Å: Chain A: M.71, N.74, Y.75, P.76, P.101, T.102, V.103, M.296 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.101, A:V.103 EDO.15: 7 residues within 4Å: Chain A: Q.23, L.57, E.262, Y.265, L.266, V.267, L.321 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.23, A:E.262, A:V.267 Water bridges: A:Q.23 EDO.19: 6 residues within 4Å: Chain B: N.47, R.61, K.62, I.63, P.64, R.300 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.47, B:R.61, B:R.300 Water bridges: B:F.65 EDO.20: 5 residues within 4Å: Chain B: G.144, H.183, A.215, P.246 Ligands: ADP.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.137 Water bridges: B:G.144 EDO.21: 1 residues within 4Å: Chain B: W.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.7 EDO.29: 3 residues within 4Å: Chain C: Y.6, W.7, Y.123 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:W.7, C:Y.123 EDO.30: 2 residues within 4Å: Chain C: I.33, E.294 No protein-ligand interaction detected (PLIP) EDO.31: 5 residues within 4Å: Chain C: T.67, K.68, S.69, R.304, D.331 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.68, C:S.69, C:R.304, C:D.331 EDO.37: 4 residues within 4Å: Chain D: R.61, K.62, P.64, R.300 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.300 EDO.38: 3 residues within 4Å: Chain D: W.7, E.8, N.116 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:W.7 Water bridges: D:E.8

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

PEG.35: 7 residues within 4Å: Chain D: S.137, F.142, H.183, I.185, G.214, A.215 Ligands: ADP.33 6 PLIP interactions: 6 interactions with chain D Water bridges: D:S.137, D:S.137, D:H.183, D:A.215, D:S.237, D:S.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of a Hypothetical Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.42 A resolution. To be published

Release Date

2014-08-27

Peptides

Phenylacetate-coenzyme A ligase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Phenylacetate-coenzyme A ligase

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