SMTL ID : 1v3w.1

Structure of Ferripyochelin binding protein from Pyrococcus horikoshii OT3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.65, H.87 Chain B: H.82, Y.159 Ligands: GOL.10 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.65, A:H.87, B:H.82, H2O.1, H2O.2 ZN.11: 5 residues within 4Å: Chain B: H.65, H.87 Chain C: H.82, Y.159 Ligands: GOL.20 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:H.82, B:H.65, B:H.87, H2O.194, H2O.195 ZN.21: 5 residues within 4Å: Chain A: H.82, Y.159 Chain C: H.65, H.87 Ligands: GOL.30 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: A:H.82, C:H.65, C:H.87, H2O.387, H2O.388

12 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.2: 8 residues within 4Å: Chain A: S.40, N.61 Chain B: S.40, N.61 Chain C: S.40, N.61 Ligands: CA.12, CA.22 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Metal complexes: B:S.40, A:S.40, C:S.40 CA.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.4: 1 residues within 4Å: Chain A: E.164 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.164, A:E.164, H2O.8, H2O.9 CA.5: 5 residues within 4Å: Chain A: N.83 Chain B: N.83 Chain C: N.83 Ligands: CA.15, CA.25 No protein-ligand interaction detected (PLIP) CA.12: 8 residues within 4Å: Chain A: S.40, N.61 Chain B: S.40, N.61 Chain C: S.40, N.61 Ligands: CA.2, CA.22 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Metal complexes: B:S.40, A:S.40, C:S.40 CA.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.14: 1 residues within 4Å: Chain B: E.164 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.164, B:E.164, H2O.201, H2O.202 CA.15: 5 residues within 4Å: Chain A: N.83 Chain B: N.83 Chain C: N.83 Ligands: CA.5, CA.25 No protein-ligand interaction detected (PLIP) CA.22: 8 residues within 4Å: Chain A: S.40, N.61 Chain B: S.40, N.61 Chain C: S.40, N.61 Ligands: CA.2, CA.12 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Metal complexes: B:S.40, C:S.40, A:S.40 CA.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.24: 1 residues within 4Å: Chain C: E.164 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.164, C:E.164, H2O.394, H2O.395 CA.25: 5 residues within 4Å: Chain A: N.83 Chain B: N.83 Chain C: N.83 Ligands: CA.5, CA.15 No protein-ligand interaction detected (PLIP)

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

CL.6: 2 residues within 4Å: Chain A: K.125, V.140 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain B: K.125, V.140 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain C: K.125, V.140 Ligand excluded by PLIP

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

EDO.7: 6 residues within 4Å: Chain A: N.22, S.40 Chain C: N.22, V.24 Ligands: EDO.17, EDO.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.40, A:S.40 EDO.8: 5 residues within 4Å: Chain A: N.22, R.172 Chain C: E.21 Ligands: EDO.18, EDO.28 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.21 EDO.9: 8 residues within 4Å: Chain A: S.100, V.102, G.118, V.120 Chain B: S.100, G.118 Ligands: EDO.19, EDO.29 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.100, A:G.118, B:S.100 EDO.17: 6 residues within 4Å: Chain A: N.22, V.24 Chain B: N.22, S.40 Ligands: EDO.7, EDO.27 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.40, B:S.40 EDO.18: 5 residues within 4Å: Chain A: E.21 Chain B: N.22, R.172 Ligands: EDO.8, EDO.28 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.21 EDO.19: 8 residues within 4Å: Chain B: S.100, V.102, G.118, V.120 Chain C: S.100, G.118 Ligands: EDO.9, EDO.29 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:S.100, B:G.118, C:S.100 EDO.27: 6 residues within 4Å: Chain B: N.22, V.24 Chain C: N.22, S.40 Ligands: EDO.7, EDO.17 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.40, C:S.40 EDO.28: 5 residues within 4Å: Chain B: E.21 Chain C: N.22, R.172 Ligands: EDO.8, EDO.18 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.21 EDO.29: 8 residues within 4Å: Chain A: S.100, G.118 Chain C: S.100, V.102, G.118, V.120 Ligands: EDO.9, EDO.19 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:S.100, C:G.118, A:S.100

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 9 residues within 4Å: Chain A: H.87 Chain B: Q.59, T.79, G.81, H.82, I.99, N.155, Y.159 Ligands: ZN.1 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.59, B:Q.59, B:H.82, B:N.155 Water bridges: B:I.99 GOL.20: 9 residues within 4Å: Chain B: H.87 Chain C: Q.59, T.79, G.81, H.82, I.99, N.155, Y.159 Ligands: ZN.11 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.59, C:Q.59, C:H.82, C:N.155 Water bridges: C:I.99 GOL.30: 9 residues within 4Å: Chain A: Q.59, T.79, G.81, H.82, I.99, N.155, Y.159 Chain C: H.87 Ligands: ZN.21 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.59, A:Q.59, A:H.82, A:N.155 Water bridges: A:I.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jeyakanthan, J. et al., Observation of a calcium-binding site in the gamma-class carbonic anhydrase from Pyrococcus horikoshii. Acta Crystallogr.,Sect.D (2008)

Release Date

2003-11-18

Peptides

ferripyochelin binding protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

ferripyochelin binding protein

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