SMTL ID : 3byq.1

Crystal structure of a duf1185 family protein (bb2672) from bordetella bronchiseptica rb50 at 1.70 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-hexamer

Ligands

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

CL.1: 6 residues within 4Å: Chain A: K.82, G.103, R.107, M.116, V.117 Ligands: EDO.5 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: K.82, R.107, V.117 Ligands: EDO.32 Ligand excluded by PLIP CL.23: 1 residues within 4Å: Chain B: R.143 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain C: K.82, G.103, R.107, V.117 Ligand excluded by PLIP CL.34: 6 residues within 4Å: Chain D: K.82, G.103, R.107, M.116, V.117 Ligands: EDO.38 Ligand excluded by PLIP CL.44: 4 residues within 4Å: Chain E: K.82, R.107, V.117 Ligands: EDO.65 Ligand excluded by PLIP CL.56: 1 residues within 4Å: Chain E: R.143 Ligand excluded by PLIP CL.57: 4 residues within 4Å: Chain F: K.82, G.103, R.107, V.117 Ligand excluded by PLIP

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

PG4.2: 9 residues within 4Å: Chain A: V.14, T.16, Y.18, K.30, T.71, L.72 Chain B: R.10, E.67 Ligands: EDO.8 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.16, A:Y.18, A:K.30 Water bridges: A:T.16, A:N.76, B:R.10 PG4.25: 8 residues within 4Å: Chain C: V.14, T.16, Y.18, K.30 Chain F: R.10, E.67 Ligands: EDO.33, EDO.66 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:Y.18, C:K.30 Water bridges: C:T.16, C:T.16, C:K.30, C:T.71, F:R.10 PG4.35: 9 residues within 4Å: Chain D: V.14, T.16, Y.18, K.30, T.71, L.72 Chain E: R.10, E.67 Ligands: EDO.41 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:Y.18, D:Y.18, D:K.30 Water bridges: D:T.16, D:T.16, D:N.76, E:R.10, E:E.67 PG4.58: 8 residues within 4Å: Chain C: R.10, E.67 Chain F: V.14, T.16, Y.18, K.30 Ligands: EDO.33, EDO.66 9 PLIP interactions: 2 interactions with chain C, 7 interactions with chain F Water bridges: C:R.10, C:E.67, F:T.16, F:K.30, F:T.71 Hydrogen bonds: F:T.16, F:Y.18, F:Y.18, F:K.30

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

EDO.3: 6 residues within 4Å: Chain A: I.13, E.15, E.150 Chain B: T.11, I.153, Q.154 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: Q.27, L.29, G.171, A.172, R.173 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: K.82, H.99, E.100, W.104 Chain D: Y.141, R.143, F.146 Ligands: CL.1 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: D.89, P.159, R.160 Chain C: D.89, P.159 Chain E: P.159, R.160 Ligand excluded by PLIP EDO.7: 10 residues within 4Å: Chain A: Y.42, A.43, G.44, R.45, Y.46, D.89, G.90, E.91, H.94 Chain D: N.21 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: L.12, T.71 Chain B: L.12 Ligands: PG4.2, EDO.18 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: L.181, R.193 Ligands: EDO.10 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: Y.141, R.193 Chain D: W.104, R.107 Ligands: EDO.9 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: I.153, Q.154 Chain B: I.13, E.15, E.150 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain B: P.25, Q.27, L.29, G.171, A.172, R.173 Ligands: EDO.17 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain B: R.58, T.62, W.104, A.105, S.108 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain B: P.23, V.174, H.175, A.176 Chain C: Y.46 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain B: A.43, G.44, R.45 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain B: Q.27, P.28, L.29, E.78, T.170, G.171 Ligands: EDO.13 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain A: L.12, E.67 Chain B: V.14, K.30, T.71 Ligands: EDO.8, EDO.22 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain B: Y.141, R.193 Chain C: W.104, R.107 Ligands: EDO.31 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain B: R.177, G.179 Chain C: M.51 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: M.2, S.3, L.4, R.39 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: R.10, E.67 Chain B: T.16, K.30 Ligands: EDO.18 Ligand excluded by PLIP EDO.26: 8 residues within 4Å: Chain B: N.21 Chain C: Y.42, G.44, R.45, Y.46, D.89, G.90, H.94 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain C: H.19, N.21, G.22 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain C: Q.27, L.29, G.171, A.172, R.173 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain B: D.190 Chain C: V.188, D.190 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain C: I.153, Q.154 Chain F: I.13, E.15, I.149, E.150 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain C: W.104, R.107, E.112 Ligands: EDO.19 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain B: K.82, H.99, W.104 Chain C: Y.141, R.143, F.146 Ligands: CL.11 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain C: L.12, T.71 Chain F: L.12 Ligands: PG4.25, PG4.58, EDO.66 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain D: I.13, E.15, E.150 Chain E: T.11, I.153, Q.154 Ligand excluded by PLIP EDO.37: 5 residues within 4Å: Chain D: Q.27, L.29, G.171, A.172, R.173 Ligand excluded by PLIP EDO.38: 8 residues within 4Å: Chain A: Y.141, R.143, F.146 Chain D: K.82, H.99, E.100, W.104 Ligands: CL.34 Ligand excluded by PLIP EDO.39: 7 residues within 4Å: Chain B: P.159, R.160 Chain D: D.89, P.159, R.160 Chain F: D.89, P.159 Ligand excluded by PLIP EDO.40: 10 residues within 4Å: Chain A: N.21 Chain D: Y.42, A.43, G.44, R.45, Y.46, D.89, G.90, E.91, H.94 Ligand excluded by PLIP EDO.41: 5 residues within 4Å: Chain D: L.12, T.71 Chain E: L.12 Ligands: PG4.35, EDO.51 Ligand excluded by PLIP EDO.42: 3 residues within 4Å: Chain D: L.181, R.193 Ligands: EDO.43 Ligand excluded by PLIP EDO.43: 5 residues within 4Å: Chain A: W.104, R.107 Chain D: Y.141, R.193 Ligands: EDO.42 Ligand excluded by PLIP EDO.45: 5 residues within 4Å: Chain D: I.153, Q.154 Chain E: I.13, E.15, E.150 Ligand excluded by PLIP EDO.46: 7 residues within 4Å: Chain E: P.25, Q.27, L.29, G.171, A.172, R.173 Ligands: EDO.50 Ligand excluded by PLIP EDO.47: 5 residues within 4Å: Chain E: R.58, T.62, W.104, A.105, S.108 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain E: P.23, V.174, H.175, A.176 Chain F: Y.46 Ligand excluded by PLIP EDO.49: 3 residues within 4Å: Chain E: A.43, G.44, R.45 Ligand excluded by PLIP EDO.50: 7 residues within 4Å: Chain E: Q.27, P.28, L.29, E.78, T.170, G.171 Ligands: EDO.46 Ligand excluded by PLIP EDO.51: 7 residues within 4Å: Chain D: L.12, E.67 Chain E: V.14, K.30, T.71 Ligands: EDO.41, EDO.55 Ligand excluded by PLIP EDO.52: 5 residues within 4Å: Chain E: Y.141, R.193 Chain F: W.104, R.107 Ligands: EDO.64 Ligand excluded by PLIP EDO.53: 3 residues within 4Å: Chain E: R.177, G.179 Chain F: M.51 Ligand excluded by PLIP EDO.54: 4 residues within 4Å: Chain E: M.2, S.3, L.4, R.39 Ligand excluded by PLIP EDO.55: 5 residues within 4Å: Chain D: R.10, E.67 Chain E: T.16, K.30 Ligands: EDO.51 Ligand excluded by PLIP EDO.59: 8 residues within 4Å: Chain E: N.21 Chain F: Y.42, G.44, R.45, Y.46, D.89, G.90, H.94 Ligand excluded by PLIP EDO.60: 3 residues within 4Å: Chain F: H.19, N.21, G.22 Ligand excluded by PLIP EDO.61: 5 residues within 4Å: Chain F: Q.27, L.29, G.171, A.172, R.173 Ligand excluded by PLIP EDO.62: 3 residues within 4Å: Chain E: D.190 Chain F: V.188, D.190 Ligand excluded by PLIP EDO.63: 6 residues within 4Å: Chain C: I.13, E.15, I.149, E.150 Chain F: I.153, Q.154 Ligand excluded by PLIP EDO.64: 4 residues within 4Å: Chain F: W.104, R.107, E.112 Ligands: EDO.52 Ligand excluded by PLIP EDO.65: 7 residues within 4Å: Chain E: K.82, H.99, W.104 Chain F: Y.141, R.143, F.146 Ligands: CL.44 Ligand excluded by PLIP EDO.66: 6 residues within 4Å: Chain C: L.12 Chain F: L.12, T.71 Ligands: PG4.25, EDO.33, PG4.58 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bakolitsa, C. et al., Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-acid metabolism. Acta Crystallogr.,Sect.F (2010)

Release Date

2008-01-29

Peptides

Uncharacterized protein DUF1185: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Uncharacterized protein DUF1185