SMTL ID : 1ekj.2 (1 other biounit)

THE X-RAY CRYSTALLOGRAPHIC STRUCTURE OF BETA CARBONIC ANHYDRASE FROM THE C3 DICOT PISUM SATIVUM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-octamer

Ligands

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

ACT.1: 10 residues within 4Å: Chain A: C.52, D.54, H.112, C.115, G.116, G.117 Chain B: Q.43, F.71, Y.97 Ligands: ZN.3 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.97 Hydrogen bonds: B:Q.43, A:D.54, A:G.116 Water bridges: B:Y.97, B:Y.97 Salt bridges: A:H.112 ACT.7: 10 residues within 4Å: Chain A: Q.43, F.71, Y.97 Chain B: C.52, D.54, V.76, C.115, G.116, G.117 Ligands: ZN.8 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:V.76, A:Y.97 Hydrogen bonds: B:D.54, B:D.54, B:G.116, B:G.117, A:Q.43, A:Y.97 Water bridges: B:R.56, B:R.56 Salt bridges: B:H.112 ACT.10: 10 residues within 4Å: Chain C: C.52, D.54, H.112, C.115, G.116, G.117 Chain D: Q.43, F.71, Y.97 Ligands: ZN.12 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:G.116, C:G.117, D:Q.43 Water bridges: C:R.56, C:R.56 Salt bridges: C:H.112 Hydrophobic interactions: D:Y.97 ACT.11: 6 residues within 4Å: Chain B: G.175, L.178, T.179 Chain C: R.184, E.185, V.188 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:R.184, C:V.188 Salt bridges: C:R.184 ACT.15: 11 residues within 4Å: Chain C: Q.43, F.71, Y.97 Chain D: C.52, D.54, V.76, H.112, C.115, G.116, G.117 Ligands: ZN.17 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:V.76, C:Y.97 Hydrogen bonds: D:G.116, C:Q.43 Water bridges: D:R.56, D:R.56 Salt bridges: D:H.112 ACT.20: 10 residues within 4Å: Chain E: C.52, D.54, H.112, C.115, G.116, G.117 Chain F: Q.43, F.71, Y.97 Ligands: ZN.22 7 PLIP interactions: 4 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:Y.97 Hydrogen bonds: F:Q.43, E:D.54, E:G.116 Water bridges: F:Y.97, F:Y.97 Salt bridges: E:H.112 ACT.26: 10 residues within 4Å: Chain E: Q.43, F.71, Y.97 Chain F: C.52, D.54, V.76, C.115, G.116, G.117 Ligands: ZN.27 11 PLIP interactions: 3 interactions with chain E, 8 interactions with chain F Hydrophobic interactions: E:Y.97, F:V.76 Hydrogen bonds: E:Q.43, E:Y.97, F:D.54, F:D.54, F:G.116, F:G.117 Water bridges: F:R.56, F:R.56 Salt bridges: F:H.112 ACT.29: 10 residues within 4Å: Chain G: C.52, D.54, H.112, C.115, G.116, G.117 Chain H: Q.43, F.71, Y.97 Ligands: ZN.31 7 PLIP interactions: 5 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:G.116, G:G.117, H:Q.43 Water bridges: G:R.56, G:R.56 Salt bridges: G:H.112 Hydrophobic interactions: H:Y.97 ACT.30: 6 residues within 4Å: Chain F: G.175, L.178, T.179 Chain G: R.184, E.185, V.188 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:R.184, G:V.188 Salt bridges: G:R.184 ACT.34: 11 residues within 4Å: Chain G: Q.43, F.71, Y.97 Chain H: C.52, D.54, V.76, H.112, C.115, G.116, G.117 Ligands: ZN.36 7 PLIP interactions: 5 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: H:V.76, G:Y.97 Hydrogen bonds: H:G.116, G:Q.43 Water bridges: H:R.56, H:R.56 Salt bridges: H:H.112

4 x AZI: AZIDE ION(Non-covalent)

AZI.2: 4 residues within 4Å: Chain A: K.140, L.143, P.144 Chain E: Y.83 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.140 AZI.16: 4 residues within 4Å: Chain D: K.140, L.143, P.144 Chain H: Y.83 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain D Water bridges: H:Q.85, D:K.140 Hydrogen bonds: D:K.140 AZI.21: 4 residues within 4Å: Chain A: Y.83 Chain E: K.140, L.143, P.144 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.140 AZI.35: 4 residues within 4Å: Chain D: Y.83 Chain H: K.140, L.143, P.144 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain D Hydrogen bonds: H:K.140, D:Y.83 Water bridges: H:K.140, D:Q.85

8 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: C.52, D.54, H.112, C.115, G.116 Ligands: ACT.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.52, A:H.112, A:C.115 ZN.8: 5 residues within 4Å: Chain B: C.52, D.54, H.112, C.115 Ligands: ACT.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.52, B:H.112, B:C.115 ZN.12: 5 residues within 4Å: Chain C: C.52, D.54, H.112, C.115 Ligands: ACT.10 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.52, C:H.112, C:C.115 ZN.17: 5 residues within 4Å: Chain D: C.52, D.54, H.112, C.115 Ligands: ACT.15 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.52, D:H.112, D:C.115 ZN.22: 6 residues within 4Å: Chain E: C.52, D.54, H.112, C.115, G.116 Ligands: ACT.20 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.52, E:H.112, E:C.115 ZN.27: 5 residues within 4Å: Chain F: C.52, D.54, H.112, C.115 Ligands: ACT.26 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.52, F:H.112, F:C.115 ZN.31: 5 residues within 4Å: Chain G: C.52, D.54, H.112, C.115 Ligands: ACT.29 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:C.52, G:H.112, G:C.115 ZN.36: 5 residues within 4Å: Chain H: C.52, D.54, H.112, C.115 Ligands: ACT.34 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:C.52, H:H.112, H:C.115

4 x CU: COPPER (II) ION(Non-covalent)

CU.4: 6 residues within 4Å: Chain A: C.58, S.60, R.74 Chain B: C.58, S.60, R.74 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:C.58, A:C.58, H2O.1 CU.13: 5 residues within 4Å: Chain C: C.58, P.59, S.60, R.74 Chain D: C.58 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.60, H2O.12, H2O.18 CU.23: 6 residues within 4Å: Chain E: C.58, S.60, R.74 Chain F: C.58, S.60, R.74 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: F:C.58, E:C.58, H2O.19 CU.32: 5 residues within 4Å: Chain G: C.58, P.59, S.60, R.74 Chain H: C.58 3 PLIP interactions: 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:S.60, H2O.29, H2O.35

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

CL.5: 3 residues within 4Å: Chain A: Y.88, G.90, T.91 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: Y.88, G.90, T.91 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain C: Y.88, G.90, T.91 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain D: Y.88, G.90, T.91 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain E: Y.88, G.90, T.91 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain F: Y.88, G.90, T.91 Ligand excluded by PLIP CL.33: 3 residues within 4Å: Chain G: Y.88, G.90, T.91 Ligand excluded by PLIP CL.37: 3 residues within 4Å: Chain H: Y.88, G.90, T.91 Ligand excluded by PLIP

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

EDO.6: 6 residues within 4Å: Chain A: P.82, I.141, P.144, N.176 Chain E: Y.83, T.179 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.141, A:N.176 EDO.19: 7 residues within 4Å: Chain D: P.82, I.141, P.144, N.176 Chain H: P.82, Y.83, T.179 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain D Water bridges: H:D.84 Hydrogen bonds: D:I.141, D:N.176 EDO.25: 6 residues within 4Å: Chain A: Y.83, T.179 Chain E: P.82, I.141, P.144, N.176 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:I.141, E:N.176 EDO.38: 7 residues within 4Å: Chain D: P.82, Y.83, T.179 Chain H: P.82, I.141, P.144, N.176 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain D Hydrogen bonds: H:I.141, H:N.176 Water bridges: D:D.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kimber, M.S. et al., The active site architecture of Pisum sativum beta-carbonic anhydrase is a mirror image of that of alpha-carbonic anhydrases. EMBO J. (2000)

Release Date

2000-06-07

Peptides

BETA-CARBONIC ANHYDRASE: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

E
E

F
F

G
G

H
H

BETA-CARBONIC ANHYDRASE

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