SMTL ID : 2hp3.1

Crystal structure of iminodisuccinate epimerase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: W.14, N.121, K.124 Ligand excluded by PLIP EDO.2: 4 residues within 4Å: Chain A: L.311, Y.312, M.313, D.314 Ligand excluded by PLIP EDO.3: 3 residues within 4Å: Chain A: Y.377, R.392, E.394 Ligand excluded by PLIP EDO.4: 2 residues within 4Å: Chain A: L.427, R.431 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: S.267, H.408, K.412, D.415 Ligands: EDO.9 Ligand excluded by PLIP EDO.6: 1 residues within 4Å: Chain A: R.138 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: G.66, W.419, M.420, P.421, E.424 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: R.433, S.434, T.436, A.437 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: S.267, W.268, H.408 Ligands: EDO.5 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: E.410, F.413, K.414, S.425, G.426, F.429 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain B: T.417, M.420, P.421, F.422, G.423, E.424, S.425 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain B: W.419, M.420, P.421 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain A: A.230, E.231 Chain B: L.146, A.147, G.148, K.308 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain B: D.405, A.407, H.408 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain B: W.14, K.15, N.121, K.124 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain B: Y.377, R.392, E.394 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain B: P.94, V.95, T.375 Ligands: PEG.44 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain B: E.307, K.308, L.310, L.311, R.362 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain B: A.13, A.16, K.17, I.18, W.256 Ligand excluded by PLIP

19 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.11: 11 residues within 4Å: Chain A: S.92, R.97, G.98, H.99 Ligands: UNX.12, UNX.13, UNX.14, UNX.15, UNX.19, UNX.21, UNX.22 Ligand excluded by PLIP UNX.12: 10 residues within 4Å: Chain A: Y.272 Ligands: UNX.11, UNX.13, UNX.14, UNX.15, UNX.16, UNX.18, UNX.20, UNX.21, UNX.22 Ligand excluded by PLIP UNX.13: 10 residues within 4Å: Chain A: S.92, R.97, T.374 Ligands: UNX.11, UNX.12, UNX.14, UNX.18, UNX.19, UNX.21, UNX.22 Ligand excluded by PLIP UNX.14: 12 residues within 4Å: Chain A: R.97, G.98, H.99 Ligands: UNX.11, UNX.12, UNX.13, UNX.15, UNX.16, UNX.17, UNX.18, UNX.21, UNX.22 Ligand excluded by PLIP UNX.15: 9 residues within 4Å: Chain A: H.99, Y.145, H.150, F.193 Ligands: UNX.11, UNX.12, UNX.14, UNX.16, UNX.17 Ligand excluded by PLIP UNX.16: 8 residues within 4Å: Chain A: Y.145, F.193, P.309 Ligands: UNX.12, UNX.14, UNX.15, UNX.17, UNX.20 Ligand excluded by PLIP UNX.17: 7 residues within 4Å: Chain A: H.99, H.150, F.193, K.198 Ligands: UNX.14, UNX.15, UNX.16 Ligand excluded by PLIP UNX.18: 8 residues within 4Å: Chain A: R.97, S.372, G.373 Ligands: UNX.12, UNX.13, UNX.14, UNX.20, UNX.22 Ligand excluded by PLIP UNX.19: 10 residues within 4Å: Chain A: S.92, F.93, P.94, R.97, G.98, T.374 Ligands: UNX.11, UNX.13, UNX.21, UNX.22 Ligand excluded by PLIP UNX.20: 9 residues within 4Å: Chain A: C.271, Y.272, A.273, P.309, G.373 Ligands: UNX.12, UNX.16, UNX.18, UNX.22 Ligand excluded by PLIP UNX.21: 9 residues within 4Å: Chain A: S.92, H.99, Y.272 Ligands: UNX.11, UNX.12, UNX.13, UNX.14, UNX.19, UNX.22 Ligand excluded by PLIP UNX.22: 11 residues within 4Å: Chain A: S.372, G.373, T.374 Ligands: UNX.11, UNX.12, UNX.13, UNX.14, UNX.18, UNX.19, UNX.20, UNX.21 Ligand excluded by PLIP UNX.33: 11 residues within 4Å: Chain B: H.99, F.193, K.198, C.271, F.323 Ligands: UNX.34, UNX.35, UNX.36, UNX.37, UNX.38, PEG.40 Ligand excluded by PLIP UNX.34: 9 residues within 4Å: Chain B: Y.145, F.193, P.309 Ligands: UNX.33, UNX.35, UNX.36, UNX.37, UNX.38, PEG.40 Ligand excluded by PLIP UNX.35: 10 residues within 4Å: Chain B: H.99, H.150, F.193, K.198 Ligands: UNX.33, UNX.34, UNX.36, UNX.37, UNX.38, UNX.39 Ligand excluded by PLIP UNX.36: 10 residues within 4Å: Chain B: H.99, Y.145, H.150, F.193 Ligands: UNX.33, UNX.34, UNX.35, UNX.37, UNX.38, UNX.39 Ligand excluded by PLIP UNX.37: 10 residues within 4Å: Chain B: R.97, H.99, Y.145 Ligands: UNX.33, UNX.34, UNX.35, UNX.36, UNX.38, UNX.39, PEG.40 Ligand excluded by PLIP UNX.38: 11 residues within 4Å: Chain B: H.99, Y.145, H.150, T.152, F.193 Ligands: UNX.33, UNX.34, UNX.35, UNX.36, UNX.37, UNX.39 Ligand excluded by PLIP UNX.39: 10 residues within 4Å: Chain B: R.97, G.98, Y.145, H.150, P.151, T.152 Ligands: UNX.35, UNX.36, UNX.37, UNX.38 Ligand excluded by PLIP

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.23: 4 residues within 4Å: Chain A: E.424, R.431, T.443, Q.445 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.424, A:R.431, A:T.443 Water bridges: A:R.431, A:R.431 PEG.40: 15 residues within 4Å: Chain B: S.92, F.93, P.94, R.97, G.98, C.271, Y.272, A.273, P.309, S.372, G.373, T.374 Ligands: UNX.33, UNX.34, UNX.37 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:F.93, B:F.93, B:G.98, B:Y.272, B:A.273, B:G.373, B:T.374 Water bridges: B:S.92, B:R.97, B:S.372 PEG.41: 11 residues within 4Å: Chain B: E.43, H.85, A.86, I.87, D.88, K.198, P.199, T.318, E.319, K.322, F.323 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.88, B:D.88, B:K.198, B:K.198 PEG.42: 3 residues within 4Å: Chain B: E.307, R.362, D.364 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.364 Water bridges: B:D.364, B:D.364 PEG.43: 5 residues within 4Å: Chain B: L.311, Y.312, M.313, D.314, P.315 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.313, B:D.314, B:D.314 PEG.44: 8 residues within 4Å: Chain B: P.94, V.95, R.97, G.137, R.138, G.141, K.142 Ligands: EDO.30 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.97, B:R.97, B:G.141, B:F.371

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lohkamp, B. et al., Three-dimensional Structure of Iminodisuccinate Epimerase Defines the Fold of the MmgE/PrpD Protein Family. J.Mol.Biol. (2006)

Release Date

2006-09-12

Peptides

IDS-epimerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

IDS-epimerase