SMTL ID : 3mdo.1

Crystal structure of a Putative phosphoribosylformylglycinamidine cyclo-ligase (BDI_2101) from Parabacteroides distasonis ATCC 8503 at 1.91 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

7 x CA: CALCIUM ION(Non-covalent)

CA.1: 1 residues within 4Å: Chain A: Q.323 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.7, H2O.7, H2O.7, H2O.7, H2O.7 CA.2: 2 residues within 4Å: Chain A: D.56 Chain B: E.147 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.56, B:E.147, H2O.5, H2O.6, H2O.18 CA.3: 5 residues within 4Å: Chain A: H.54, D.56, M.88, D.92 Ligands: PGE.15 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.56, A:D.92, H2O.9, H2O.9 CA.4: 2 residues within 4Å: Chain B: D.56 Ligands: ACT.23 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.56, H2O.7, H2O.8, H2O.17 CA.17: 5 residues within 4Å: Chain B: H.54, D.56, M.88, D.92 Ligands: ACT.23 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.56, B:D.92, H2O.14, H2O.16, H2O.18 CA.18: 2 residues within 4Å: Chain B: Q.323 Ligands: CAC.22 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:Q.323, H2O.17, H2O.17, H2O.17, H2O.17 CA.19: 1 residues within 4Å: Chain B: G.146 No protein-ligand interaction detected (PLIP)

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 5 residues within 4Å: Chain A: R.110, K.112, D.150, V.151, G.152 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: C.288, N.336 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain B: R.110, K.112, D.150, V.151, G.152 Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain B: N.336 Ligand excluded by PLIP

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 7 residues within 4Å: Chain A: S.106, I.108, I.124, G.145, G.146, E.147, T.148 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.108 Hydrogen bonds: A:T.148 Water bridges: A:G.146, A:G.146, A:G.146 ACT.23: 8 residues within 4Å: Chain B: D.56, M.88, N.207, S.289, G.290, K.295 Ligands: CA.4, CA.17 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.207 Water bridges: B:D.92, B:D.92, B:D.92, B:S.289, B:K.295

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

PEG.8: 5 residues within 4Å: Chain A: I.30, F.31, P.32, D.175, K.177 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.177 PEG.9: 5 residues within 4Å: Chain A: Q.321, D.327, W.328, S.329, F.387 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.321, A:W.328, A:S.329, A:S.329 Water bridges: A:D.327 PEG.10: 4 residues within 4Å: Chain A: E.301, N.302, K.375, N.376 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.302, A:N.302, A:N.376 Water bridges: A:N.376 PEG.11: 7 residues within 4Å: Chain A: G.182, D.183, V.184, F.369, V.370, E.371 Ligands: PGE.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.182 Water bridges: A:E.371 PEG.12: 2 residues within 4Å: Chain A: Y.220, K.244 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.244 PEG.13: 6 residues within 4Å: Chain A: S.171, V.173, I.174, R.279, S.280, I.282 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.282, A:I.282 Water bridges: A:N.178 PEG.24: 5 residues within 4Å: Chain B: T.210, H.214, D.215, V.233, L.237 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.215 PEG.25: 4 residues within 4Å: Chain B: D.41, I.42, G.45, P.47 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.142 PEG.26: 5 residues within 4Å: Chain B: E.133, T.195, Y.196, E.197, K.198 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.197 PEG.27: 1 residues within 4Å: Chain B: K.277 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.277 PEG.28: 2 residues within 4Å: Chain B: R.386, T.388 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.386, B:T.388

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

PGE.14: 3 residues within 4Å: Chain A: I.366, F.369 Ligands: PEG.11 No protein-ligand interaction detected (PLIP) PGE.15: 7 residues within 4Å: Chain A: F.35, H.54, D.92, K.295, H.298, F.299 Ligands: CA.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.54 PGE.29: 1 residues within 4Å: Chain B: K.112 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.112 PGE.30: 7 residues within 4Å: Chain B: F.35, H.54, D.92, G.290, K.295, H.298, F.299 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.54, B:K.295 Water bridges: B:H.54 PGE.31: 4 residues within 4Å: Chain B: G.242, L.243, E.322, Q.323 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.323

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.16: 10 residues within 4Å: Chain A: T.210, S.211, H.214, D.215, V.233, L.237, S.324, T.326, M.331, F.335 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.211, A:S.324, A:S.324 Water bridges: A:D.215

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.22: 5 residues within 4Å: Chain B: D.215, S.240, Q.323, S.324 Ligands: CA.18 No protein-ligand interaction detected (PLIP)

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.32: 3 residues within 4Å: Chain B: E.71, Y.220, K.244 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.244 PG4.33: 4 residues within 4Å: Chain B: K.70, K.112, L.113, P.116 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.70

Links

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Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of a Putative phosphoribosylformylglycinamidine cyclo-ligase (BDI_2101) from Parabacteroides distasonis ATCC 8503 at 1.91 A resolution. To be published

Release Date

2010-06-02

Peptides

Putative phosphoribosylformylglycinamidine cyclo-ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative phosphoribosylformylglycinamidine cyclo-ligase