SMTL ID : 2dho.1

Crystal structure of human IPP isomerase I in space group P212121

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

8 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.1: 5 residues within 4Å: Chain A: H.48, H.59, H.96, E.154, E.156 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.48, A:H.59, A:H.96, A:E.154, A:E.156 MN.2: 2 residues within 4Å: Chain A: H.143, H.155 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.143, A:H.155, H2O.1, H2O.2, H2O.2, H2O.3 MN.3: 1 residues within 4Å: Chain A: K.145 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:K.145, H2O.1, H2O.1, H2O.1, H2O.1, H2O.1 MN.4: 3 residues within 4Å: Chain A: Y.144, E.156, D.158 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.144, A:E.156, A:D.158, H2O.2, H2O.7 MN.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MN.6: 7 residues within 4Å: Chain A: Q.76, T.92, C.93, R.119, L.120, E.123, L.124 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.93, A:E.123 MN.7: 3 residues within 4Å: Chain A: F.85, C.88, I.201 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.88, H2O.11 MN.8: 2 residues within 4Å: Chain A: E.105, S.107 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.105, A:S.107, H2O.12, H2O.12, H2O.12

2 x NA: SODIUM ION(Non-functional Binders)

NA.9: 4 residues within 4Å: Chain A: P.171, S.178, Y.179 Ligands: CL.11 No protein-ligand interaction detected (PLIP) NA.10: 5 residues within 4Å: Chain A: D.218, N.219, L.220, N.221, H.222 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.218, A:N.221

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

CL.11: 3 residues within 4Å: Chain A: S.178, Y.179 Ligands: NA.9 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: K.121, P.127, L.128 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: N.71, K.184 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: N.71, R.164, N.221 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain A: H.222, N.224, Q.225 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain A: F.85, A.146, T.202, P.203, W.204 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain A: N.52 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain A: K.44 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain A: A.194, A.195, K.206 Ligand excluded by PLIP CL.20: 1 residues within 4Å: Chain A: E.135 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, C. et al., Crystal structures of human IPP isomerase: new insights into the catalytic mechanism. J.Mol.Biol. (2007)

Release Date

2007-06-05

Peptides

Isopentenyl-diphosphate delta-isomerase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Isopentenyl-diphosphate delta-isomerase 1

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