SMTL ID : 4izg.1

Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound cis-4oh-d-proline betaine (product)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-octamer

Ligands

108 x IOD: IODIDE ION(Non-functional Binders)

IOD.1: 3 residues within 4Å: Chain A: W.68, K.136 Ligands: IOD.2 Ligand excluded by PLIP IOD.2: 4 residues within 4Å: Chain A: L.65, A.66, K.136 Ligands: IOD.1 Ligand excluded by PLIP IOD.3: 2 residues within 4Å: Chain A: A.79, S.81 Ligand excluded by PLIP IOD.4: 5 residues within 4Å: Chain A: Q.53, G.75, P.76, H.82, A.83 Ligand excluded by PLIP IOD.5: 1 residues within 4Å: Chain A: A.88 Ligand excluded by PLIP IOD.6: 1 residues within 4Å: Chain A: E.197 Ligand excluded by PLIP IOD.7: 2 residues within 4Å: Chain A: R.254, G.255 Ligand excluded by PLIP IOD.8: 3 residues within 4Å: Chain A: Q.335, P.336, R.337 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: Y.158, G.161, Y.348 Ligand excluded by PLIP IOD.10: 1 residues within 4Å: Chain A: H.29 Ligand excluded by PLIP IOD.11: 1 residues within 4Å: Chain A: V.387 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain A: R.110 Chain B: A.150 Ligand excluded by PLIP IOD.17: 2 residues within 4Å: Chain B: Q.335, R.337 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain B: G.99, R.111 Ligand excluded by PLIP IOD.19: 3 residues within 4Å: Chain B: L.65, A.66, K.136 Ligand excluded by PLIP IOD.20: 2 residues within 4Å: Chain B: W.68, K.136 Ligand excluded by PLIP IOD.21: 1 residues within 4Å: Ligands: IOD.22 Ligand excluded by PLIP IOD.22: 2 residues within 4Å: Chain B: A.88 Ligands: IOD.21 Ligand excluded by PLIP IOD.23: 2 residues within 4Å: Chain B: A.79, S.81 Ligand excluded by PLIP IOD.24: 5 residues within 4Å: Chain B: Q.53, G.75, P.76, H.82, A.83 Ligand excluded by PLIP IOD.25: 2 residues within 4Å: Chain B: A.362, G.363 Ligand excluded by PLIP IOD.26: 3 residues within 4Å: Chain B: Y.158, T.160, G.161 Ligand excluded by PLIP IOD.27: 3 residues within 4Å: Chain B: G.163, Q.164, E.167 Ligand excluded by PLIP IOD.28: 5 residues within 4Å: Chain B: E.193, R.228 Chain F: W.203, G.208, G.210 Ligand excluded by PLIP IOD.29: 1 residues within 4Å: Chain B: E.197 Ligand excluded by PLIP IOD.30: 2 residues within 4Å: Chain B: R.254, G.255 Ligand excluded by PLIP IOD.31: 2 residues within 4Å: Chain A: A.150 Chain B: R.110 Ligand excluded by PLIP IOD.35: 3 residues within 4Å: Chain C: W.68, K.136 Ligands: IOD.36 Ligand excluded by PLIP IOD.36: 4 residues within 4Å: Chain C: L.65, A.66, K.136 Ligands: IOD.35 Ligand excluded by PLIP IOD.37: 2 residues within 4Å: Chain C: A.79, S.81 Ligand excluded by PLIP IOD.38: 5 residues within 4Å: Chain C: Q.53, G.75, P.76, H.82, A.83 Ligand excluded by PLIP IOD.39: 1 residues within 4Å: Chain C: A.88 Ligand excluded by PLIP IOD.40: 1 residues within 4Å: Chain C: E.197 Ligand excluded by PLIP IOD.41: 2 residues within 4Å: Chain C: R.254, G.255 Ligand excluded by PLIP IOD.42: 3 residues within 4Å: Chain C: Q.335, P.336, R.337 Ligand excluded by PLIP IOD.43: 3 residues within 4Å: Chain C: Y.158, G.161, Y.348 Ligand excluded by PLIP IOD.44: 1 residues within 4Å: Chain C: H.29 Ligand excluded by PLIP IOD.45: 1 residues within 4Å: Chain C: V.387 Ligand excluded by PLIP IOD.46: 2 residues within 4Å: Chain C: R.110 Chain D: A.150 Ligand excluded by PLIP IOD.51: 2 residues within 4Å: Chain D: Q.335, R.337 Ligand excluded by PLIP IOD.52: 2 residues within 4Å: Chain D: G.99, R.111 Ligand excluded by PLIP IOD.53: 3 residues within 4Å: Chain D: L.65, A.66, K.136 Ligand excluded by PLIP IOD.54: 2 residues within 4Å: Chain D: W.68, K.136 Ligand excluded by PLIP IOD.55: 1 residues within 4Å: Ligands: IOD.56 Ligand excluded by PLIP IOD.56: 2 residues within 4Å: Chain D: A.88 Ligands: IOD.55 Ligand excluded by PLIP IOD.57: 2 residues within 4Å: Chain D: A.79, S.81 Ligand excluded by PLIP IOD.58: 5 residues within 4Å: Chain D: Q.53, G.75, P.76, H.82, A.83 Ligand excluded by PLIP IOD.59: 2 residues within 4Å: Chain D: A.362, G.363 Ligand excluded by PLIP IOD.60: 3 residues within 4Å: Chain D: Y.158, T.160, G.161 Ligand excluded by PLIP IOD.61: 3 residues within 4Å: Chain D: G.163, Q.164, E.167 Ligand excluded by PLIP IOD.62: 5 residues within 4Å: Chain D: E.193, R.228 Chain H: W.203, G.208, G.210 Ligand excluded by PLIP IOD.63: 1 residues within 4Å: Chain D: E.197 Ligand excluded by PLIP IOD.64: 2 residues within 4Å: Chain D: R.254, G.255 Ligand excluded by PLIP IOD.65: 2 residues within 4Å: Chain C: A.150 Chain D: R.110 Ligand excluded by PLIP IOD.69: 3 residues within 4Å: Chain E: W.68, K.136 Ligands: IOD.70 Ligand excluded by PLIP IOD.70: 4 residues within 4Å: Chain E: L.65, A.66, K.136 Ligands: IOD.69 Ligand excluded by PLIP IOD.71: 2 residues within 4Å: Chain E: A.79, S.81 Ligand excluded by PLIP IOD.72: 5 residues within 4Å: Chain E: Q.53, G.75, P.76, H.82, A.83 Ligand excluded by PLIP IOD.73: 1 residues within 4Å: Chain E: A.88 Ligand excluded by PLIP IOD.74: 1 residues within 4Å: Chain E: E.197 Ligand excluded by PLIP IOD.75: 2 residues within 4Å: Chain E: R.254, G.255 Ligand excluded by PLIP IOD.76: 3 residues within 4Å: Chain E: Q.335, P.336, R.337 Ligand excluded by PLIP IOD.77: 3 residues within 4Å: Chain E: Y.158, G.161, Y.348 Ligand excluded by PLIP IOD.78: 1 residues within 4Å: Chain E: H.29 Ligand excluded by PLIP IOD.79: 1 residues within 4Å: Chain E: V.387 Ligand excluded by PLIP IOD.80: 2 residues within 4Å: Chain E: R.110 Chain F: A.150 Ligand excluded by PLIP IOD.85: 2 residues within 4Å: Chain F: Q.335, R.337 Ligand excluded by PLIP IOD.86: 2 residues within 4Å: Chain F: G.99, R.111 Ligand excluded by PLIP IOD.87: 3 residues within 4Å: Chain F: L.65, A.66, K.136 Ligand excluded by PLIP IOD.88: 2 residues within 4Å: Chain F: W.68, K.136 Ligand excluded by PLIP IOD.89: 1 residues within 4Å: Ligands: IOD.90 Ligand excluded by PLIP IOD.90: 2 residues within 4Å: Chain F: A.88 Ligands: IOD.89 Ligand excluded by PLIP IOD.91: 2 residues within 4Å: Chain F: A.79, S.81 Ligand excluded by PLIP IOD.92: 5 residues within 4Å: Chain F: Q.53, G.75, P.76, H.82, A.83 Ligand excluded by PLIP IOD.93: 2 residues within 4Å: Chain F: A.362, G.363 Ligand excluded by PLIP IOD.94: 3 residues within 4Å: Chain F: Y.158, T.160, G.161 Ligand excluded by PLIP IOD.95: 3 residues within 4Å: Chain F: G.163, Q.164, E.167 Ligand excluded by PLIP IOD.96: 5 residues within 4Å: Chain D: W.203, G.208, G.210 Chain F: E.193, R.228 Ligand excluded by PLIP IOD.97: 1 residues within 4Å: Chain F: E.197 Ligand excluded by PLIP IOD.98: 2 residues within 4Å: Chain F: R.254, G.255 Ligand excluded by PLIP IOD.99: 2 residues within 4Å: Chain E: A.150 Chain F: R.110 Ligand excluded by PLIP IOD.103: 3 residues within 4Å: Chain G: W.68, K.136 Ligands: IOD.104 Ligand excluded by PLIP IOD.104: 4 residues within 4Å: Chain G: L.65, A.66, K.136 Ligands: IOD.103 Ligand excluded by PLIP IOD.105: 2 residues within 4Å: Chain G: A.79, S.81 Ligand excluded by PLIP IOD.106: 5 residues within 4Å: Chain G: Q.53, G.75, P.76, H.82, A.83 Ligand excluded by PLIP IOD.107: 1 residues within 4Å: Chain G: A.88 Ligand excluded by PLIP IOD.108: 1 residues within 4Å: Chain G: E.197 Ligand excluded by PLIP IOD.109: 2 residues within 4Å: Chain G: R.254, G.255 Ligand excluded by PLIP IOD.110: 3 residues within 4Å: Chain G: Q.335, P.336, R.337 Ligand excluded by PLIP IOD.111: 3 residues within 4Å: Chain G: Y.158, G.161, Y.348 Ligand excluded by PLIP IOD.112: 1 residues within 4Å: Chain G: H.29 Ligand excluded by PLIP IOD.113: 1 residues within 4Å: Chain G: V.387 Ligand excluded by PLIP IOD.114: 2 residues within 4Å: Chain G: R.110 Chain H: A.150 Ligand excluded by PLIP IOD.119: 2 residues within 4Å: Chain H: Q.335, R.337 Ligand excluded by PLIP IOD.120: 2 residues within 4Å: Chain H: G.99, R.111 Ligand excluded by PLIP IOD.121: 3 residues within 4Å: Chain H: L.65, A.66, K.136 Ligand excluded by PLIP IOD.122: 2 residues within 4Å: Chain H: W.68, K.136 Ligand excluded by PLIP IOD.123: 1 residues within 4Å: Ligands: IOD.124 Ligand excluded by PLIP IOD.124: 2 residues within 4Å: Chain H: A.88 Ligands: IOD.123 Ligand excluded by PLIP IOD.125: 2 residues within 4Å: Chain H: A.79, S.81 Ligand excluded by PLIP IOD.126: 5 residues within 4Å: Chain H: Q.53, G.75, P.76, H.82, A.83 Ligand excluded by PLIP IOD.127: 2 residues within 4Å: Chain H: A.362, G.363 Ligand excluded by PLIP IOD.128: 3 residues within 4Å: Chain H: Y.158, T.160, G.161 Ligand excluded by PLIP IOD.129: 3 residues within 4Å: Chain H: G.163, Q.164, E.167 Ligand excluded by PLIP IOD.130: 5 residues within 4Å: Chain B: W.203, G.208, G.210 Chain H: E.193, R.228 Ligand excluded by PLIP IOD.131: 1 residues within 4Å: Chain H: E.197 Ligand excluded by PLIP IOD.132: 2 residues within 4Å: Chain H: R.254, G.255 Ligand excluded by PLIP IOD.133: 2 residues within 4Å: Chain G: A.150 Chain H: R.110 Ligand excluded by PLIP

20 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.14: 7 residues within 4Å: Chain A: Y.78, Q.184, D.216, N.218, E.241, D.264 Ligands: 4OP.16 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.216, A:E.241, A:D.264, H2O.1, 4OP.16 MG.15: 2 residues within 4Å: Chain A: A.26, S.391 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.391, A:S.391, H2O.3 MG.32: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.33: 7 residues within 4Å: Chain B: Y.78, Q.184, D.216, N.218, E.241, D.264 Ligands: 4OP.34 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:D.216, B:E.241, B:D.264, H2O.17, 4OP.34 MG.47: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.48: 7 residues within 4Å: Chain C: Y.78, Q.184, D.216, N.218, E.241, D.264 Ligands: 4OP.50 5 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: C:D.216, C:E.241, C:D.264, H2O.31, 4OP.50 MG.49: 2 residues within 4Å: Chain C: A.26, S.391 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.391, C:S.391, H2O.33 MG.66: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.67: 7 residues within 4Å: Chain D: Y.78, Q.184, D.216, N.218, E.241, D.264 Ligands: 4OP.68 5 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: D:D.216, D:E.241, D:D.264, H2O.47, 4OP.68 MG.81: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.82: 7 residues within 4Å: Chain E: Y.78, Q.184, D.216, N.218, E.241, D.264 Ligands: 4OP.84 5 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: E:D.216, E:E.241, E:D.264, H2O.61, 4OP.84 MG.83: 2 residues within 4Å: Chain E: A.26, S.391 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:S.391, E:S.391, H2O.63 MG.100: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.101: 7 residues within 4Å: Chain F: Y.78, Q.184, D.216, N.218, E.241, D.264 Ligands: 4OP.102 5 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: F:D.216, F:E.241, F:D.264, H2O.77, 4OP.102 MG.115: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.116: 7 residues within 4Å: Chain G: Y.78, Q.184, D.216, N.218, E.241, D.264 Ligands: 4OP.118 5 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: G:D.216, G:E.241, G:D.264, H2O.91, 4OP.118 MG.117: 2 residues within 4Å: Chain G: A.26, S.391 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:S.391, G:S.391, H2O.93 MG.134: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.135: 7 residues within 4Å: Chain H: Y.78, Q.184, D.216, N.218, E.241, D.264 Ligands: 4OP.136 5 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H:D.216, H:E.241, H:D.264, H2O.108, 4OP.136

8 x 4OP: (2S,4S)-2-carboxy-4-hydroxy-1,1-dimethylpyrrolidinium(Non-covalent)

4OP.16: 15 residues within 4Å: Chain A: V.74, Y.78, Y.157, A.159, Q.184, K.186, D.216, N.218, E.241, D.264, K.288, D.316, A.317, W.343 Ligands: MG.14 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.78 Hydrogen bonds: A:Y.157, A:Q.184, A:D.216, A:N.218, A:A.317 Water bridges: A:D.264, A:S.313 Salt bridges: A:K.186, A:K.288 pi-Cation interactions: A:W.343, A:W.343 4OP.34: 15 residues within 4Å: Chain B: V.74, Y.78, Y.157, A.159, Q.184, K.186, D.216, N.218, E.241, D.264, K.288, D.316, A.317, W.343 Ligands: MG.33 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.78 Hydrogen bonds: B:Y.78, B:Y.157, B:Q.184, B:N.218, B:A.317 Water bridges: B:D.315, B:D.315 Salt bridges: B:K.186, B:K.288 pi-Cation interactions: B:W.343, B:W.343 4OP.50: 15 residues within 4Å: Chain C: V.74, Y.78, Y.157, A.159, Q.184, K.186, D.216, N.218, E.241, D.264, K.288, D.316, A.317, W.343 Ligands: MG.48 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:Y.78 Hydrogen bonds: C:Y.157, C:Q.184, C:D.216, C:N.218, C:A.317 Water bridges: C:D.264, C:S.313 Salt bridges: C:K.186, C:K.288 pi-Cation interactions: C:W.343, C:W.343 4OP.68: 15 residues within 4Å: Chain D: V.74, Y.78, Y.157, A.159, Q.184, K.186, D.216, N.218, E.241, D.264, K.288, D.316, A.317, W.343 Ligands: MG.67 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:Y.78 Hydrogen bonds: D:Y.78, D:Y.157, D:Q.184, D:N.218, D:A.317 Water bridges: D:D.315, D:D.315 Salt bridges: D:K.186, D:K.288 pi-Cation interactions: D:W.343, D:W.343 4OP.84: 15 residues within 4Å: Chain E: V.74, Y.78, Y.157, A.159, Q.184, K.186, D.216, N.218, E.241, D.264, K.288, D.316, A.317, W.343 Ligands: MG.82 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:Y.78 Hydrogen bonds: E:Y.157, E:Q.184, E:D.216, E:N.218, E:A.317 Water bridges: E:D.264, E:S.313 Salt bridges: E:K.186, E:K.288 pi-Cation interactions: E:W.343, E:W.343 4OP.102: 15 residues within 4Å: Chain F: V.74, Y.78, Y.157, A.159, Q.184, K.186, D.216, N.218, E.241, D.264, K.288, D.316, A.317, W.343 Ligands: MG.101 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:Y.78 Hydrogen bonds: F:Y.78, F:Y.157, F:Q.184, F:N.218, F:A.317 Water bridges: F:D.315, F:D.315 Salt bridges: F:K.186, F:K.288 pi-Cation interactions: F:W.343, F:W.343 4OP.118: 15 residues within 4Å: Chain G: V.74, Y.78, Y.157, A.159, Q.184, K.186, D.216, N.218, E.241, D.264, K.288, D.316, A.317, W.343 Ligands: MG.116 12 PLIP interactions: 12 interactions with chain G Hydrophobic interactions: G:Y.78 Hydrogen bonds: G:Y.157, G:Q.184, G:D.216, G:N.218, G:A.317 Water bridges: G:D.264, G:S.313 Salt bridges: G:K.186, G:K.288 pi-Cation interactions: G:W.343, G:W.343 4OP.136: 15 residues within 4Å: Chain H: V.74, Y.78, Y.157, A.159, Q.184, K.186, D.216, N.218, E.241, D.264, K.288, D.316, A.317, W.343 Ligands: MG.135 12 PLIP interactions: 12 interactions with chain H Hydrophobic interactions: H:Y.78 Hydrogen bonds: H:Y.78, H:Y.157, H:Q.184, H:N.218, H:A.317 Water bridges: H:D.315, H:D.315 Salt bridges: H:K.186, H:K.288 pi-Cation interactions: H:W.343, H:W.343

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, R. et al., Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine. MBio (2014)

Release Date

2013-02-13

Peptides

Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein

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