SMTL ID : 2yeq.3 (2 other biounits)

Structure of PhoD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-dimer

Ligands

30 x PE5: 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL(Non-covalent)

PE5.1: 4 residues within 4Å: Chain A: G.319, F.365, S.368, K.369 Ligand excluded by PLIP PE5.2: 5 residues within 4Å: Chain A: E.54, V.101, A.197, A.200 Ligands: PE5.37 Ligand excluded by PLIP PE5.3: 5 residues within 4Å: Chain A: P.294, Y.347, D.353, P.356, R.359 Ligand excluded by PLIP PE5.6: 8 residues within 4Å: Chain A: R.444, T.446, Q.451, K.453, D.455, S.474, V.487, S.488 Ligand excluded by PLIP PE5.8: 5 residues within 4Å: Chain A: I.177, A.230, R.234 Chain B: N.302 Ligands: NA.87 Ligand excluded by PLIP PE5.14: 5 residues within 4Å: Chain A: E.54, H.55, F.56, R.91, V.101 Ligand excluded by PLIP PE5.20: 5 residues within 4Å: Chain A: S.251, Q.260, Y.262, R.263, W.313 Ligand excluded by PLIP PE5.21: 4 residues within 4Å: Chain A: E.223, K.224, G.225, N.288 Ligand excluded by PLIP PE5.22: 4 residues within 4Å: Chain A: K.52, K.58, I.59, V.60 Ligand excluded by PLIP PE5.23: 8 residues within 4Å: Chain A: P.2, N.3, F.4, S.5, S.6, P.31, G.38, P.40 Ligand excluded by PLIP PE5.24: 3 residues within 4Å: Chain A: T.165, G.166, N.167 Ligand excluded by PLIP PE5.32: 7 residues within 4Å: Chain A: N.219, K.220, V.228 Chain B: N.219, K.220, V.228, V.232 Ligand excluded by PLIP PE5.36: 3 residues within 4Å: Chain A: K.68, S.70, L.71 Ligand excluded by PLIP PE5.37: 3 residues within 4Å: Chain A: Y.89, K.103 Ligands: PE5.2 Ligand excluded by PLIP PE5.44: 4 residues within 4Å: Chain B: G.319, F.365, S.368, K.369 Ligand excluded by PLIP PE5.45: 6 residues within 4Å: Chain B: E.54, V.101, A.197, A.200, A.201 Ligands: PE5.81 Ligand excluded by PLIP PE5.46: 6 residues within 4Å: Chain B: P.294, Y.347, D.353, P.356, R.359, E.394 Ligand excluded by PLIP PE5.49: 7 residues within 4Å: Chain B: Q.116, R.444, T.446, Q.451, K.453, D.455, V.487 Ligand excluded by PLIP PE5.51: 4 residues within 4Å: Chain A: N.302 Chain B: I.177, A.230 Ligands: NA.43 Ligand excluded by PLIP PE5.53: 7 residues within 4Å: Chain B: R.472, K.486, V.487, S.488, S.489, T.491 Ligands: EDO.73 Ligand excluded by PLIP PE5.57: 4 residues within 4Å: Chain B: E.54, H.55, R.91, V.101 Ligand excluded by PLIP PE5.63: 4 residues within 4Å: Chain B: S.251, Q.260, Y.262, R.263 Ligand excluded by PLIP PE5.64: 4 residues within 4Å: Chain A: E.297 Chain B: E.223, K.224, N.288 Ligand excluded by PLIP PE5.65: 4 residues within 4Å: Chain B: K.52, K.58, I.59, V.60 Ligand excluded by PLIP PE5.66: 3 residues within 4Å: Chain B: I.59, V.60, K.62 Ligand excluded by PLIP PE5.67: 8 residues within 4Å: Chain B: P.2, N.3, F.4, S.5, S.6, P.31, G.38, P.40 Ligand excluded by PLIP PE5.68: 1 residues within 4Å: Chain B: N.167 Ligand excluded by PLIP PE5.74: 3 residues within 4Å: Chain B: K.52, E.83, K.86 Ligand excluded by PLIP PE5.80: 4 residues within 4Å: Chain B: K.68, S.70, L.71 Ligands: EDO.71 Ligand excluded by PLIP PE5.81: 6 residues within 4Å: Chain B: E.54, Y.89, K.103, A.201, F.202 Ligands: PE5.45 Ligand excluded by PLIP

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

EDO.4: 5 residues within 4Å: Chain A: P.158, H.171, N.172, A.174 Ligands: EDO.17 Ligand excluded by PLIP EDO.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: D.17, P.18, L.19, R.249, R.263 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: K.142, L.143, D.144 Ligands: EDO.26 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: D.283, D.284, R.303 Chain B: G.225, Q.226, S.227, V.228 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: N.291, F.339, E.503, E.504 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: D.418, Y.439, R.472, T.491, I.492, G.495, K.497 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: T.178, Q.180, D.181 Ligands: EDO.17, EDO.29 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: I.177, L.233, R.234 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: E.65, M.66, K.68, L.71, S.74, V.75, H.76 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: S.173, A.174, D.181 Ligands: EDO.4, EDO.13, EDO.29 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain A: K.336, S.342, E.394, E.429, P.431 Ligands: EDO.35 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: Y.161, V.162, H.382, G.413, R.506, S.509 Ligand excluded by PLIP EDO.25: 2 residues within 4Å: Chain A: I.433, Q.434 Ligand excluded by PLIP EDO.26: 9 residues within 4Å: Chain A: K.103, T.104, K.105, L.143, D.144, A.201, F.202, P.203 Ligands: EDO.9 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain A: L.71, L.253, P.254 Ligands: EDO.28 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain A: Q.240, P.254, N.255, G.256 Ligands: EDO.27 Ligand excluded by PLIP EDO.29: 7 residues within 4Å: Chain A: N.172, S.173, Q.180, D.181, N.184 Ligands: EDO.13, EDO.17 Ligand excluded by PLIP EDO.30: 2 residues within 4Å: Chain A: K.486, S.489 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain A: S.191, D.192, A.193 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain A: H.264, T.266, S.272, N.317, S.320, S.321 Ligand excluded by PLIP EDO.35: 8 residues within 4Å: Chain A: K.336, H.390, F.393, E.394, T.396, P.431, H.432 Ligands: EDO.18 Ligand excluded by PLIP EDO.47: 4 residues within 4Å: Chain B: H.171, N.172, S.173, A.174 Ligand excluded by PLIP EDO.48: 4 residues within 4Å: Chain B: N.415, F.461, T.463, E.464 Ligand excluded by PLIP EDO.50: 6 residues within 4Å: Chain B: D.17, L.19, R.249, R.263, H.264, F.265 Ligand excluded by PLIP EDO.52: 4 residues within 4Å: Chain B: K.142, L.143, D.144 Ligands: EDO.70 Ligand excluded by PLIP EDO.54: 4 residues within 4Å: Chain B: N.291, F.339, E.503, E.504 Ligand excluded by PLIP EDO.55: 7 residues within 4Å: Chain B: D.418, Y.439, R.472, T.491, I.492, G.495, K.497 Ligand excluded by PLIP EDO.56: 5 residues within 4Å: Chain B: T.178, Q.180, D.181 Ligands: EDO.60, EDO.72 Ligand excluded by PLIP EDO.58: 3 residues within 4Å: Chain B: I.177, L.233, R.234 Ligand excluded by PLIP EDO.59: 7 residues within 4Å: Chain B: E.65, M.66, K.68, L.71, S.74, V.75, H.76 Ligand excluded by PLIP EDO.60: 4 residues within 4Å: Chain B: S.173, A.174, D.181 Ligands: EDO.56 Ligand excluded by PLIP EDO.61: 4 residues within 4Å: Chain B: S.342, E.429, P.431 Ligands: EDO.79 Ligand excluded by PLIP EDO.62: 5 residues within 4Å: Chain B: Y.161, H.382, G.413, E.501, R.506 Ligand excluded by PLIP EDO.69: 2 residues within 4Å: Chain B: I.433, Q.434 Ligand excluded by PLIP EDO.70: 9 residues within 4Å: Chain B: K.103, T.104, K.105, L.143, D.144, A.201, F.202, P.203 Ligands: EDO.52 Ligand excluded by PLIP EDO.71: 3 residues within 4Å: Chain B: L.253, P.254 Ligands: PE5.80 Ligand excluded by PLIP EDO.72: 6 residues within 4Å: Chain B: N.172, S.173, Q.180, D.181, N.184 Ligands: EDO.56 Ligand excluded by PLIP EDO.73: 3 residues within 4Å: Chain B: K.486, S.489 Ligands: PE5.53 Ligand excluded by PLIP EDO.75: 4 residues within 4Å: Chain B: S.191, D.192, A.193, N.194 Ligand excluded by PLIP EDO.76: 3 residues within 4Å: Chain B: D.258, M.259, Q.260 Ligand excluded by PLIP EDO.77: 6 residues within 4Å: Chain B: H.264, T.266, S.272, N.317, S.320, S.321 Ligand excluded by PLIP EDO.79: 8 residues within 4Å: Chain B: K.336, F.393, E.394, T.396, E.429, P.431, H.432 Ligands: EDO.61 Ligand excluded by PLIP

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

NA.34: 2 residues within 4Å: Chain A: D.284, Q.285 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.284 NA.38: 3 residues within 4Å: Chain A: E.175, E.214, Q.517 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.517, A:Q.517 NA.43: 5 residues within 4Å: Chain A: N.300, N.302 Chain B: Q.226, S.227 Ligands: PE5.51 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.300, A:N.300, A:N.302, B:S.227 NA.78: 2 residues within 4Å: Chain B: D.284, Q.285 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.284, B:Q.285 NA.82: 3 residues within 4Å: Chain B: E.175, E.214, Q.517 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.214, B:Q.517, B:Q.517 NA.87: 5 residues within 4Å: Chain A: Q.226, S.227 Chain B: N.300, N.302 Ligands: PE5.8 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.300, B:N.300, B:N.302, A:S.227

2 x FE: FE (III) ION(Non-covalent)

FE.39: 6 residues within 4Å: Chain A: C.124, D.151, Y.154, H.382 Ligands: CA.40, PO4.42 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.124, A:D.151, A:Y.154, A:H.382 FE.83: 6 residues within 4Å: Chain B: C.124, D.151, Y.154, H.382 Ligands: CA.84, PO4.86 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.124, B:D.151, B:Y.154, B:H.382

4 x CA: CALCIUM ION(Non-covalent)

CA.40: 6 residues within 4Å: Chain A: D.151, D.209, D.210, D.380 Ligands: FE.39, PO4.42 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.151, A:D.151, A:D.209, A:D.210, A:D.380 CA.41: 5 residues within 4Å: Chain A: D.210, H.211, N.215, N.216 Ligands: PO4.42 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.210, H2O.9, H2O.12 CA.84: 6 residues within 4Å: Chain B: D.151, D.209, D.210, D.380 Ligands: FE.83, PO4.86 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.151, B:D.209, B:D.210, B:D.380, H2O.17 CA.85: 5 residues within 4Å: Chain B: D.210, H.211, N.215, N.216 Ligands: PO4.86 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.210, H2O.21, H2O.24

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.42: 12 residues within 4Å: Chain A: C.124, D.151, Y.154, D.210, H.211, D.380, H.382, R.506, H.510 Ligands: FE.39, CA.40, CA.41 6 PLIP interactions: 6 interactions with chain A Water bridges: A:D.380, A:R.506 Salt bridges: A:H.211, A:H.382, A:R.506, A:H.510 PO4.86: 12 residues within 4Å: Chain B: C.124, D.151, Y.154, D.210, H.211, D.380, H.382, R.506, H.510 Ligands: FE.83, CA.84, CA.85 8 PLIP interactions: 8 interactions with chain B Water bridges: B:D.380, B:R.506, B:R.506, B:R.506 Salt bridges: B:H.211, B:H.382, B:R.506, B:H.510

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rodriguez, F. et al., Crystal Structure of the Bacillus Subtilis Phosphodiesterase Phod Reveals an Iron and Calcium-Containing Active Site. J.Biol.Chem. (2014)

Release Date

2012-04-18

Peptides

ALKALINE PHOSPHATASE D: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ALKALINE PHOSPHATASE D

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