SMTL ID : 3i4p.1

Crystal structure of AsnC family transcriptional regulator from Agrobacterium tumefaciens

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-octamer

Ligands

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

CL.1: 2 residues within 4Å: Chain A: R.48, R.49 Ligand excluded by PLIP CL.2: 5 residues within 4Å: Chain A: D.112, I.113 Chain H: D.112, I.113 Ligands: CL.51 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain E: R.49, R.50 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: S.16 Chain E: S.16 Ligands: CL.32 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: S.99, G.100 Chain D: V.132, S.134 Ligands: CA.5 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: R.48, R.49 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain B: D.112, I.113 Chain G: D.112, I.113 Ligands: CL.44 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain F: R.49, R.50 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: S.16 Chain F: S.16 Ligands: CL.39 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain B: S.99, G.100 Chain C: V.132, S.134 Ligands: CA.12 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain C: R.48, R.49 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain C: D.112, I.113 Chain F: D.112, I.113 Ligands: CL.37 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain H: R.49, R.50 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain C: S.16 Chain H: S.16 Ligands: CL.53 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain A: V.132, S.134 Chain C: S.99, G.100 Ligands: CA.19 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain D: R.48, R.49 Ligand excluded by PLIP CL.23: 5 residues within 4Å: Chain D: D.112, I.113 Chain E: D.112, I.113 Ligands: CL.30 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain G: R.49, R.50 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain D: S.16 Chain G: S.16 Ligands: CL.46 Ligand excluded by PLIP CL.27: 5 residues within 4Å: Chain B: V.132, S.134 Chain D: S.99, G.100 Ligands: CA.26 Ligand excluded by PLIP CL.29: 2 residues within 4Å: Chain E: R.48, R.49 Ligand excluded by PLIP CL.30: 5 residues within 4Å: Chain D: D.112, I.113 Chain E: D.112, I.113 Ligands: CL.23 Ligand excluded by PLIP CL.31: 2 residues within 4Å: Chain A: R.49, R.50 Ligand excluded by PLIP CL.32: 3 residues within 4Å: Chain A: S.16 Chain E: S.16 Ligands: CL.4 Ligand excluded by PLIP CL.34: 5 residues within 4Å: Chain E: S.99, G.100 Chain H: V.132, S.134 Ligands: CA.33 Ligand excluded by PLIP CL.36: 2 residues within 4Å: Chain F: R.48, R.49 Ligand excluded by PLIP CL.37: 5 residues within 4Å: Chain C: D.112, I.113 Chain F: D.112, I.113 Ligands: CL.16 Ligand excluded by PLIP CL.38: 2 residues within 4Å: Chain B: R.49, R.50 Ligand excluded by PLIP CL.39: 3 residues within 4Å: Chain B: S.16 Chain F: S.16 Ligands: CL.11 Ligand excluded by PLIP CL.41: 5 residues within 4Å: Chain F: S.99, G.100 Chain G: V.132, S.134 Ligands: CA.40 Ligand excluded by PLIP CL.43: 2 residues within 4Å: Chain G: R.48, R.49 Ligand excluded by PLIP CL.44: 5 residues within 4Å: Chain B: D.112, I.113 Chain G: D.112, I.113 Ligands: CL.9 Ligand excluded by PLIP CL.45: 2 residues within 4Å: Chain D: R.49, R.50 Ligand excluded by PLIP CL.46: 3 residues within 4Å: Chain D: S.16 Chain G: S.16 Ligands: CL.25 Ligand excluded by PLIP CL.48: 5 residues within 4Å: Chain E: V.132, S.134 Chain G: S.99, G.100 Ligands: CA.47 Ligand excluded by PLIP CL.50: 2 residues within 4Å: Chain H: R.48, R.49 Ligand excluded by PLIP CL.51: 5 residues within 4Å: Chain A: D.112, I.113 Chain H: D.112, I.113 Ligands: CL.2 Ligand excluded by PLIP CL.52: 2 residues within 4Å: Chain C: R.49, R.50 Ligand excluded by PLIP CL.53: 3 residues within 4Å: Chain C: S.16 Chain H: S.16 Ligands: CL.18 Ligand excluded by PLIP CL.55: 5 residues within 4Å: Chain F: V.132, S.134 Chain H: S.99, G.100 Ligands: CA.54 Ligand excluded by PLIP

8 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: G.100, D.103 Chain D: V.132 Ligands: CL.6 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: D:V.132, A:G.100, H2O.3, H2O.3, H2O.4 CA.12: 4 residues within 4Å: Chain B: G.100, D.103 Chain C: V.132 Ligands: CL.13 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: B:G.100, C:V.132, H2O.8, H2O.8, H2O.8 CA.19: 4 residues within 4Å: Chain A: V.132 Chain C: G.100, D.103 Ligands: CL.20 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: C:G.100, A:V.132, H2O.12, H2O.12, H2O.13 CA.26: 4 residues within 4Å: Chain B: V.132 Chain D: G.100, D.103 Ligands: CL.27 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: D:G.100, B:V.132, H2O.17, H2O.17, H2O.17 CA.33: 4 residues within 4Å: Chain E: G.100, D.103 Chain H: V.132 Ligands: CL.34 5 PLIP interactions: 1 interactions with chain H, 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: H:V.132, E:G.100, H2O.21, H2O.21, H2O.22 CA.40: 4 residues within 4Å: Chain F: G.100, D.103 Chain G: V.132 Ligands: CL.41 5 PLIP interactions: 1 interactions with chain G, 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: G:V.132, F:G.100, H2O.26, H2O.26, H2O.26 CA.47: 4 residues within 4Å: Chain E: V.132 Chain G: G.100, D.103 Ligands: CL.48 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: E:V.132, G:G.100, H2O.30, H2O.30, H2O.31 CA.54: 4 residues within 4Å: Chain F: V.132 Chain H: G.100, D.103 Ligands: CL.55 5 PLIP interactions: 1 interactions with chain F, 1 interactions with chain H, 3 Ligand-Water interactions Metal complexes: F:V.132, H:G.100, H2O.35, H2O.35, H2O.35

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

ACT.7: 7 residues within 4Å: Chain A: T.71, A.72, D.103 Chain D: I.129, R.130, D.131, V.132 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:D.103 Water bridges: D:V.132 ACT.14: 7 residues within 4Å: Chain B: T.71, A.72, D.103 Chain C: I.129, R.130, D.131, V.132 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:D.103 Water bridges: C:V.132 ACT.21: 7 residues within 4Å: Chain A: I.129, R.130, D.131, V.132 Chain C: T.71, A.72, D.103 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Water bridges: A:V.132 Hydrogen bonds: C:D.103 ACT.28: 7 residues within 4Å: Chain B: I.129, R.130, D.131, V.132 Chain D: T.71, A.72, D.103 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:D.103 Water bridges: B:V.132 ACT.35: 7 residues within 4Å: Chain E: T.71, A.72, D.103 Chain H: I.129, R.130, D.131, V.132 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain E Water bridges: H:Y.120 Hydrogen bonds: E:D.103 ACT.42: 7 residues within 4Å: Chain F: T.71, A.72, D.103 Chain G: I.129, R.130, D.131, V.132 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:D.103 Water bridges: G:Y.120 ACT.49: 7 residues within 4Å: Chain E: I.129, R.130, D.131, V.132 Chain G: T.71, A.72, D.103 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain E Hydrogen bonds: G:D.103 Water bridges: E:Y.120 ACT.56: 7 residues within 4Å: Chain F: I.129, R.130, D.131, V.132 Chain H: T.71, A.72, D.103 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain H Water bridges: F:Y.120 Hydrogen bonds: H:D.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cymborowski, M. et al., Crystal structure of AsnC family transcriptional regulator from Agrobacterium tumefaciens. To be Published

Release Date

2009-07-28

Peptides

Transcriptional regulator, AsnC family: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

Transcriptional regulator, AsnC family