SMTL ID : 4rvo.2 (1 other biounit)

Crystal structure of a Putative Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.41 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-dimer

Ligands

2 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.12: 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

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

ADP.2: 18 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: K.3, UNL.5 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:A.215, A:S.237, A:G.239, A:T.241, A:T.241, A:D.305, A:R.329, A:G.338 Water bridges: A:T.143, A:G.144, A:G.144, A:N.236, A:T.241, A:T.241, A:N.340, A:N.340 ADP.11: 16 residues within 4Å: Chain B: S.94, 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: UNL.14 17 PLIP interactions: 17 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:G.144, B:N.236, B:N.236, B:T.303, B:R.329 Salt bridges: B:K.425, B:K.425

3 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain A: A.215, I.335, G.338, N.340 Ligands: ADP.2 No protein-ligand interaction detected (PLIP) K.4: 8 residues within 4Å: Chain A: M.84, K.85, R.86, G.88 Chain B: K.129, G.156, C.157, L.158 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:K.85, A:G.88, B:K.129, B:G.156 K.13: 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

2 x UNL: UNKNOWN LIGAND

UNL.5: 12 residues within 4Å: Chain A: S.137, G.138, F.142, G.144, A.215, G.239, P.246, K.337, G.338, L.406, T.408 Ligands: ADP.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.137, A:S.137, A:G.138, A:G.239, A:K.337, A:K.337, A:K.337, A:G.338, A:L.406, A:T.408 Water bridges: A:S.137, A:S.137, A:H.183, A:S.237 UNL.14: 10 residues within 4Å: Chain B: S.137, G.138, F.142, G.144, F.148, H.183, A.215, G.239, P.246 Ligands: ADP.11 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.137, B:S.137, B:G.138, B:H.183, B:H.183 Water bridges: B:G.144, B:G.144, B:H.183, B:H.183, B:G.214

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

SO4.6: 5 residues within 4Å: Chain A: G.165, N.166, S.167, Y.188, R.191 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.166, A:S.167 Salt bridges: A:R.191 SO4.15: 4 residues within 4Å: Chain B: G.165, N.166, S.167, R.191 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.166, B:S.167, B:S.167, B:S.167 Water bridges: B:K.168 Salt bridges: B:R.191

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

PGE.7: 5 residues within 4Å: Chain A: W.7, E.8, N.116, R.154 Ligands: EDO.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.116, A:R.154, A:R.154

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

EDO.8: 2 residues within 4Å: Chain A: Y.123 Ligands: PGE.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.123 EDO.9: 3 residues within 4Å: Chain A: R.61, K.62, P.64 No protein-ligand interaction detected (PLIP) EDO.10: 4 residues within 4Å: Chain A: T.67, K.68, S.69, R.304 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.69, A:R.304 EDO.16: 3 residues within 4Å: Chain B: W.7, E.8, N.116 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.7 Water bridges: B:E.8, B:N.116 EDO.17: 2 residues within 4Å: Chain B: Y.150, R.154 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:Y.150, B:R.154 EDO.18: 4 residues within 4Å: Chain B: R.61, K.62, P.64, R.300 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.300 Water bridges: B:G.275, B:R.300

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of a Putative Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.41 A resolution. To be published

Release Date

2014-12-31

Peptides

Phenylacetate-coenzyme A ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Phenylacetate-coenzyme A ligase

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