SMTL ID : 5bv2.1

Crystal structure of E. coli HPII catalase variant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

homo-tetramer

Ligands

4 x HDD: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE(Non-covalent)

HDD.1: 33 residues within 4Å: Chain A: R.125, I.126, V.127, H.128, R.165, S.167, G.184, F.185, A.186, V.199, G.200, N.201, F.206, I.208, A.211, F.214, G.273, I.274, H.275, P.356, F.391, L.407, G.410, R.411, S.414, Y.415, T.418, Q.419, R.422 Chain D: I.114, F.117, D.118 Ligands: GOL.2 27 PLIP interactions: 27 interactions with chain A, Hydrophobic interactions: A:R.125, A:H.128, A:V.199, A:N.201, A:F.206, A:F.206, A:F.214, A:F.214, A:F.214, A:F.214, A:L.407, A:L.407, A:R.411, A:Y.415, A:Y.415, A:T.418 Hydrogen bonds: A:S.414, A:Q.419 Water bridges: A:R.125, A:R.165 Salt bridges: A:R.125, A:R.165, A:R.422 pi-Stacking: A:H.128, A:F.214 pi-Cation interactions: A:R.411 Metal complexes: A:Y.415 HDD.19: 33 residues within 4Å: Chain B: R.125, I.126, V.127, H.128, R.165, S.167, G.184, F.185, A.186, V.199, G.200, N.201, F.206, I.208, A.211, F.214, G.273, I.274, H.275, P.356, F.391, L.407, G.410, R.411, S.414, Y.415, T.418, Q.419, R.422 Chain C: I.114, F.117, D.118 Ligands: GOL.20 30 PLIP interactions: 30 interactions with chain B, Hydrophobic interactions: B:R.125, B:V.127, B:H.128, B:A.186, B:V.199, B:N.201, B:F.206, B:F.206, B:F.214, B:F.214, B:F.214, B:F.214, B:L.407, B:L.407, B:R.411, B:Y.415, B:Y.415, B:T.418 Hydrogen bonds: B:S.414, B:Q.419 Water bridges: B:R.125, B:R.165, B:A.186 Salt bridges: B:R.125, B:R.165, B:R.422 pi-Stacking: B:H.128, B:F.214 pi-Cation interactions: B:R.411 Metal complexes: B:Y.415 HDD.44: 33 residues within 4Å: Chain B: I.114, F.117, D.118 Chain C: R.125, I.126, V.127, H.128, R.165, S.167, G.184, F.185, A.186, V.199, G.200, N.201, F.206, I.208, A.211, F.214, G.273, I.274, H.275, P.356, F.391, L.407, G.410, R.411, S.414, Y.415, T.418, Q.419, R.422 Ligands: GOL.45 29 PLIP interactions: 29 interactions with chain C, Hydrophobic interactions: C:R.125, C:H.128, C:V.199, C:N.201, C:F.206, C:F.206, C:F.214, C:F.214, C:F.214, C:F.214, C:L.407, C:L.407, C:R.411, C:Y.415, C:Y.415, C:T.418 Hydrogen bonds: C:S.414, C:Q.419 Water bridges: C:R.125, C:R.165, C:A.186 Salt bridges: C:R.125, C:R.165, C:R.422 pi-Stacking: C:H.128, C:F.206, C:F.214 pi-Cation interactions: C:R.411 Metal complexes: C:Y.415 HDD.56: 33 residues within 4Å: Chain A: I.114, F.117, D.118 Chain D: R.125, I.126, V.127, H.128, R.165, S.167, G.184, F.185, A.186, V.199, G.200, N.201, F.206, I.208, A.211, F.214, G.273, I.274, H.275, P.356, F.391, L.407, G.410, R.411, S.414, Y.415, T.418, Q.419, R.422 Ligands: GOL.57 27 PLIP interactions: 27 interactions with chain D, Hydrophobic interactions: D:R.125, D:H.128, D:V.199, D:N.201, D:F.206, D:F.206, D:F.214, D:F.214, D:F.214, D:F.214, D:L.407, D:L.407, D:R.411, D:Y.415, D:Y.415, D:T.418 Hydrogen bonds: D:S.414, D:Q.419 Water bridges: D:R.125, D:R.165 Salt bridges: D:R.125, D:R.165, D:R.422 pi-Stacking: D:H.128, D:F.214 pi-Cation interactions: D:R.411 Metal complexes: D:Y.415

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: V.127, H.128, V.169, I.182, N.201, F.206, F.214, F.217, V.218 Ligands: HDD.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.128, A:N.201 GOL.13: 7 residues within 4Å: Chain A: R.121, A.173, F.382, F.383, E.387 Chain C: D.446 Chain D: A.228 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.387 Water bridges: A:R.121, A:R.125 GOL.20: 10 residues within 4Å: Chain B: V.127, H.128, V.169, I.182, N.201, F.206, F.214, F.217, V.218 Ligands: HDD.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.128, B:N.201 GOL.38: 4 residues within 4Å: Chain B: T.574, P.575, P.576, P.577 No protein-ligand interaction detected (PLIP) GOL.39: 4 residues within 4Å: Chain B: A.282, S.283, P.477 Ligands: EDO.31 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.478 GOL.45: 10 residues within 4Å: Chain C: V.127, H.128, V.169, I.182, N.201, F.206, F.214, F.217, V.218 Ligands: HDD.44 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.128, C:N.201, C:N.201 GOL.52: 9 residues within 4Å: Chain B: R.100 Chain C: E.346, F.347, F.349, D.350, F.351, D.352, L.353, S.500 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Water bridges: C:F.347, C:F.349, C:S.500, B:R.100 GOL.53: 8 residues within 4Å: Chain A: R.488 Chain B: G.491, N.492, V.494, E.496 Chain C: G.98, D.99, R.100 7 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B, 3 interactions with chain C Hydrogen bonds: A:R.488, B:N.492, B:N.492, B:E.496, C:D.99, C:D.99 Water bridges: C:R.100 GOL.57: 10 residues within 4Å: Chain D: V.127, H.128, V.169, I.182, N.201, F.206, F.214, F.217, V.218 Ligands: HDD.56 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.128, D:N.201, D:N.201 GOL.67: 6 residues within 4Å: Chain D: D.609, Y.634, R.636, V.640, T.641, D.674 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.636, D:R.636 GOL.68: 7 residues within 4Å: Chain A: G.491, N.492, V.494, E.496 Chain B: R.488 Chain D: G.98, D.99 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 4 interactions with chain A Hydrogen bonds: B:R.488, D:D.99, A:N.492, A:N.492 Water bridges: A:E.496, A:E.496

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

EDO.3: 7 residues within 4Å: Chain A: G.98, D.99 Chain C: R.488 Chain D: G.491, N.492, V.494, E.496 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: T.516, S.589, Y.591, A.592 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: P.517, F.518, R.521, I.745 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: K.709, S.750, P.752 Chain D: A.676, D.677, N.682, T.707 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: Y.634, S.635, F.654, D.674, I.675, N.678 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: D.155, N.157, K.158, I.159, E.192 Ligand excluded by PLIP EDO.9: 11 residues within 4Å: Chain A: A.176, V.179, R.180, Q.231, G.232, Q.233, W.304, Q.308, T.311 Chain D: G.312, P.315 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: P.594, D.595, G.596, A.737, A.738 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain A: E.346, F.347, K.348, F.349, D.350, F.351, D.352, S.500 Ligand excluded by PLIP EDO.21: 12 residues within 4Å: Chain A: I.465 Chain B: E.224, H.226, W.227, H.236, D.237, T.238, V.535, R.536 Chain C: P.49, T.50 Ligands: PEG.40 Ligand excluded by PLIP EDO.22: 8 residues within 4Å: Chain B: G.98, D.99, R.100 Chain C: G.491, N.492, V.494, E.496 Chain D: R.488 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: R.61, N.62, E.63, N.66 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain B: R.61, E.69 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain B: R.542 Chain C: H.12, Q.13, S.14, P.15, P.31, E.32 Ligand excluded by PLIP EDO.26: 10 residues within 4Å: Chain B: A.176, V.179, Q.231, G.232, Q.233, W.304, Q.308, T.311 Chain C: G.312, P.315 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain B: L.620, L.623, K.624, V.628, H.629, A.630 Ligand excluded by PLIP EDO.28: 9 residues within 4Å: Chain B: W.469, R.471, E.472, T.473, P.474 Chain D: Y.78, A.79, L.80, R.87 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain B: Q.139, P.140, Y.141, P.156, N.372 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain B: P.575, P.576, P.577, D.578, K.583 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain B: S.145, D.146, N.281, A.282, S.283 Ligands: GOL.39 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain B: H.441 Chain D: R.72, K.73, G.74, Y.78 Ligand excluded by PLIP EDO.33: 7 residues within 4Å: Chain B: G.34, S.35, R.37, P.38, A.39, A.40, Q.48 Ligand excluded by PLIP EDO.34: 7 residues within 4Å: Chain B: S.35, A.47, Q.48, P.49 Chain C: V.535, R.536, P.537 Ligand excluded by PLIP EDO.35: 1 residues within 4Å: Chain B: F.347 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain B: N.682, T.707 Chain C: K.709, S.750, P.752 Ligand excluded by PLIP EDO.37: 6 residues within 4Å: Chain B: V.598, K.626, D.730, L.733, T.734, A.737 Ligand excluded by PLIP EDO.46: 7 residues within 4Å: Chain C: R.521, I.745, P.746, K.747, I.748, D.749 Ligands: PGE.50 Ligand excluded by PLIP EDO.47: 7 residues within 4Å: Chain C: W.512, P.517, Q.520, R.521, V.524, T.553, A.557 Ligand excluded by PLIP EDO.48: 11 residues within 4Å: Chain B: G.312, P.315 Chain C: A.176, V.179, R.180, Q.231, G.232, Q.233, W.304, Q.308, T.311 Ligand excluded by PLIP EDO.49: 5 residues within 4Å: Chain C: S.613, A.614, L.617, D.643, D.644 Ligand excluded by PLIP EDO.58: 7 residues within 4Å: Chain B: A.79, R.87 Chain D: W.469, R.471, E.472, T.473, P.474 Ligand excluded by PLIP EDO.59: 7 residues within 4Å: Chain D: V.303, D.305, K.690, H.691, L.692, I.748 Ligands: EDO.60 Ligand excluded by PLIP EDO.60: 8 residues within 4Å: Chain D: V.303, R.521, H.522, D.525, L.692, I.745, I.748 Ligands: EDO.59 Ligand excluded by PLIP EDO.61: 3 residues within 4Å: Chain D: L.620, A.630, L.632 Ligand excluded by PLIP EDO.62: 3 residues within 4Å: Chain D: G.284, Y.485, Q.486 Ligand excluded by PLIP EDO.63: 7 residues within 4Å: Chain B: V.71, K.73 Chain D: E.430, R.435, Y.440, M.451, G.452 Ligand excluded by PLIP EDO.64: 6 residues within 4Å: Chain D: N.8, P.9, H.10, Q.11, H.12 Ligands: SO4.69 Ligand excluded by PLIP EDO.65: 9 residues within 4Å: Chain A: V.535, R.536, P.537, Y.538 Chain D: S.35, H.36, A.47, Q.48, P.49 Ligand excluded by PLIP EDO.66: 4 residues within 4Å: Chain D: T.516, P.517, F.518, A.592 Ligand excluded by PLIP

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.12: 8 residues within 4Å: Chain A: S.613, L.616, L.617, L.620, L.632, T.646, L.648, P.649 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.646, A:T.646 PGE.50: 12 residues within 4Å: Chain C: V.303, D.305, E.306, R.521, H.522, D.525, K.690, H.691, L.692, I.745, I.748 Ligands: EDO.46 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.522 Water bridges: C:R.521, C:D.525 PGE.51: 9 residues within 4Å: Chain C: K.149, N.281, A.282, G.284, P.475, G.476, P.477, E.483, Q.486 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.282, C:Q.486 Water bridges: C:K.149, C:E.483

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

PEG.14: 12 residues within 4Å: Chain A: D.305, K.309, Y.683, E.687, K.690, H.691, A.753 Chain D: K.309, R.313, A.655, D.680, Y.683 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:D.305, A:K.309, A:K.690, A:H.691, D:R.313, D:D.680 Water bridges: A:Y.683, D:R.313, D:R.313 PEG.15: 5 residues within 4Å: Chain A: K.348, F.349, L.364, V.365, N.580 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.348, A:L.364 Water bridges: A:N.580 PEG.16: 9 residues within 4Å: Chain A: K.142, S.143, L.144, D.146, I.147, L.340, Q.368, R.369, V.370 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.142, A:D.146, A:I.147, A:R.369 Water bridges: A:S.143, A:D.146 PEG.17: 13 residues within 4Å: Chain A: R.264, L.302, E.306, L.310, F.317, R.601, L.660, T.661, V.662, D.663, K.693, H.739, R.740 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.264, A:R.601, A:T.661, A:D.663, A:D.663, A:H.739, A:R.740, A:R.740 PEG.40: 10 residues within 4Å: Chain B: W.227, I.229, P.230, Q.233, A.235, H.236, D.237, K.533 Chain C: R.320 Ligands: EDO.21 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:R.320, C:R.320 Water bridges: B:Q.233, B:D.237, B:K.533, B:K.533 PEG.41: 6 residues within 4Å: Chain B: N.77, Y.78, A.79, R.87 Chain D: P.439, H.441 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:A.79 Water bridges: B:R.87, B:R.87, D:P.439 PEG.42: 6 residues within 4Å: Chain B: K.299, E.362, P.586, S.587, I.593, D.595 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.299, B:E.362, B:D.595 Water bridges: B:S.587 PEG.43: 8 residues within 4Å: Chain B: K.142, L.144, D.146, I.147, L.340, Q.368, R.369, V.370 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.142 Water bridges: B:D.146, B:R.369 PEG.71: 10 residues within 4Å: Chain A: R.320 Chain D: W.227, I.229, P.230, Q.233, A.235, H.236, D.237, K.533, V.535 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain A Water bridges: D:E.224, D:Q.233, D:Q.233, D:D.237, D:D.237, D:K.533, D:K.533, A:D.314 Hydrogen bonds: A:R.320, A:R.320 PEG.72: 7 residues within 4Å: Chain D: K.149, N.281, A.282, P.475, G.476, P.477, E.483 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.282, D:E.483 Water bridges: D:G.284

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.18: 5 residues within 4Å: Chain A: R.72, K.73, G.74, Y.78 Chain C: H.441 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.72, A:G.74, A:Y.78 Water bridges: A:K.73 Salt bridges: A:K.73, C:H.441 SO4.69: 7 residues within 4Å: Chain A: R.542 Chain D: H.12, Q.13, P.31, E.32, D.33 Ligands: EDO.64 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:E.32, A:R.542 Water bridges: D:H.12, D:Q.13 Salt bridges: D:H.12

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

MG.54: 1 residues within 4Å: Chain C: E.63 No protein-ligand interaction detected (PLIP) MG.70: 1 residues within 4Å: Chain D: E.32 No protein-ligand interaction detected (PLIP)

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.55: 5 residues within 4Å: Chain C: S.143, S.145, D.146, S.154, K.478 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.143, C:S.145, C:S.154 Water bridges: C:S.154, C:K.478, C:K.478

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J. et al., Influence of weak-intensity data, ordered water molecules, and hydrogen atoms on the refinement of a large protein crystal structure. To be Published

Release Date

2015-06-24

Peptides

Catalase HPII: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
P

B
Q

C
R

D
S

Catalase HPII