SMTL ID : 2hek.1

Crystal structure of O67745, a hypothetical protein from Aquifex aeolicus at 2.0 A resolution.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 10 residues within 4Å: Chain A: Q.36, R.51, H.54, H.84, D.85, H.88, D.161, Y.165 Ligands: ZN.2, GOL.10 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.36, A:D.161 Water bridges: A:H.88 Salt bridges: A:R.51, A:H.84, A:H.88 PO4.13: 9 residues within 4Å: Chain B: R.51, H.54, H.84, D.85, H.88, D.161, Y.165 Ligands: ZN.16, GOL.21 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.36 Water bridges: B:H.84, B:H.84, B:D.161 Salt bridges: B:R.51, B:H.84 PO4.14: 5 residues within 4Å: Chain A: F.12 Chain B: G.174, V.175, S.176, Y.177 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.176 Water bridges: B:G.174, B:Y.177, A:G.11 PO4.15: 5 residues within 4Å: Chain B: E.73, K.74, E.75, L.76, Y.126 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.75, B:L.76, B:Y.126 PO4.23: 10 residues within 4Å: Chain C: Q.36, R.51, H.54, H.84, D.85, H.88, D.161, Y.165 Ligands: ZN.24, GOL.32 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.36, C:D.85, C:D.161 Salt bridges: C:R.51, C:H.84, C:H.88 PO4.35: 9 residues within 4Å: Chain D: R.51, H.54, H.84, D.85, H.88, D.161, Y.165 Ligands: ZN.38, GOL.43 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.36 Water bridges: D:H.84, D:D.161 Salt bridges: D:R.51, D:H.84 PO4.36: 5 residues within 4Å: Chain C: F.12 Chain D: G.174, V.175, S.176, Y.177 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.176 Water bridges: D:G.174, C:G.11 PO4.37: 5 residues within 4Å: Chain D: E.73, K.74, E.75, L.76, Y.126 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.75, D:L.76

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.54, H.84, D.85, D.161 Ligands: PO4.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.54, A:D.85, A:D.161, H2O.1 ZN.16: 5 residues within 4Å: Chain B: H.54, H.84, D.85, D.161 Ligands: PO4.13 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.54, B:D.161, H2O.7 ZN.24: 5 residues within 4Å: Chain C: H.54, H.84, D.85, D.161 Ligands: PO4.23 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.54, C:D.85, C:D.161, H2O.14 ZN.38: 5 residues within 4Å: Chain D: H.54, H.84, D.85, D.161 Ligands: PO4.35 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.54, D:D.161, H2O.21

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

CL.3: 4 residues within 4Å: Chain A: G.16, G.19, Y.59, E.75 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: G.38, L.39, F.91, S.92 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: G.38, L.39, S.92 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain B: R.162, Y.165, R.213, Y.217 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain B: Y.10, H.60, R.64, Y.182 Ligand excluded by PLIP CL.25: 4 residues within 4Å: Chain C: G.16, G.19, Y.59, E.75 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain C: G.38, L.39, F.91, S.92 Ligand excluded by PLIP CL.40: 3 residues within 4Å: Chain D: G.38, L.39, S.92 Ligand excluded by PLIP CL.41: 4 residues within 4Å: Chain D: R.162, Y.165, R.213, Y.217 Ligand excluded by PLIP CL.42: 4 residues within 4Å: Chain D: Y.10, H.60, R.64, Y.182 Ligand excluded by PLIP

4 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.5: 15 residues within 4Å: Chain A: L.42, V.43, P.45, V.225, R.280, H.282 Chain B: K.3, E.4, F.5, I.23, D.24, Q.29, R.32, F.52 Ligands: GOL.8 14 PLIP interactions: 8 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:K.3, B:Q.29, B:R.32, B:R.32, A:R.280 Water bridges: B:E.4, A:R.280 Salt bridges: B:K.3, B:K.3, B:D.24, A:R.280, A:H.282, A:H.282 pi-Cation interactions: A:R.280 GDP.6: 14 residues within 4Å: Chain A: K.3, E.4, F.5, L.20, D.24, Q.29, R.32, F.52 Chain B: L.42, V.43, V.225, R.280, H.282 Ligands: GOL.7 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.3, A:D.24, A:Q.29, A:R.32, A:R.32 Salt bridges: A:K.3, A:K.3, A:D.24, B:H.282 pi-Stacking: A:F.5 Water bridges: B:H.282 GDP.27: 15 residues within 4Å: Chain C: L.42, V.43, P.45, V.225, R.280, H.282 Chain D: K.3, E.4, F.5, I.23, D.24, Q.29, R.32, F.52 Ligands: GOL.30 14 PLIP interactions: 8 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:K.3, D:Q.29, D:R.32, D:R.32, C:R.280 Water bridges: D:E.4, C:R.280 Salt bridges: D:K.3, D:K.3, D:D.24, C:R.280, C:H.282, C:H.282 pi-Cation interactions: C:R.280 GDP.28: 14 residues within 4Å: Chain C: K.3, E.4, F.5, L.20, D.24, Q.29, R.32, F.52 Chain D: L.42, V.43, V.225, R.280, H.282 Ligands: GOL.29 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:K.3, C:Q.29, C:R.32, C:R.32 Salt bridges: C:K.3, C:K.3, C:D.24, D:H.282 pi-Stacking: C:F.5

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: E.4, F.5, S.6, F.12 Chain B: V.43, F.44, H.223 Ligands: GDP.6 Ligand excluded by PLIP GOL.8: 8 residues within 4Å: Chain A: V.43, F.44, H.223 Chain B: E.4, F.5, S.6, F.12 Ligands: GDP.5 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain A: R.167, A.170, Y.171, G.178, F.179, F.180 Ligand excluded by PLIP GOL.10: 6 residues within 4Å: Chain A: Q.36, L.37, Y.165, D.169, Y.221 Ligands: PO4.1 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain A: F.278, Q.279 Chain B: D.24, F.26, Q.29 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain A: Y.10, I.61, R.167, F.180, D.181, Y.182, D.183 Ligand excluded by PLIP GOL.21: 6 residues within 4Å: Chain B: Q.36, L.37, R.51, Y.165, D.169 Ligands: PO4.13 Ligand excluded by PLIP GOL.22: 11 residues within 4Å: Chain B: Y.177, F.179, N.208, I.211, S.212, F.215 Chain C: Y.177, G.178, F.179, N.208, I.211 Ligand excluded by PLIP GOL.29: 8 residues within 4Å: Chain C: E.4, F.5, S.6, F.12 Chain D: V.43, F.44, H.223 Ligands: GDP.28 Ligand excluded by PLIP GOL.30: 8 residues within 4Å: Chain C: V.43, F.44, H.223 Chain D: E.4, F.5, S.6, F.12 Ligands: GDP.27 Ligand excluded by PLIP GOL.31: 6 residues within 4Å: Chain C: R.167, A.170, Y.171, G.178, F.179, F.180 Ligand excluded by PLIP GOL.32: 6 residues within 4Å: Chain C: Q.36, L.37, Y.165, D.169, Y.221 Ligands: PO4.23 Ligand excluded by PLIP GOL.33: 5 residues within 4Å: Chain C: F.278, Q.279 Chain D: D.24, F.26, Q.29 Ligand excluded by PLIP GOL.34: 7 residues within 4Å: Chain C: Y.10, I.61, R.167, F.180, D.181, Y.182, D.183 Ligand excluded by PLIP GOL.43: 6 residues within 4Å: Chain D: Q.36, L.37, R.51, Y.165, D.169 Ligands: PO4.35 Ligand excluded by PLIP GOL.44: 11 residues within 4Å: Chain A: Y.177, G.178, F.179, N.208, I.211 Chain D: Y.177, F.179, N.208, I.211, S.212, F.215 Ligand excluded by PLIP

2 x BR: BROMIDE ION(Non-covalent)

BR.17: 4 residues within 4Å: Chain B: G.16, G.19, Y.59, E.75 Ligand excluded by PLIP BR.39: 4 residues within 4Å: Chain D: G.16, G.19, Y.59, E.75 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oganesyan, V. et al., Structure of O67745_AQUAE, a hypothetical protein from Aquifex aeolicus. Acta Crystallogr.,Sect.F (2007)

Release Date

2006-07-04

Peptides

Hypothetical protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Hypothetical protein