- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- homo-trimer
- Ligands
- 3 x CU1: COPPER (I) ION(Non-covalent)
- 2 x SX: SULFUR OXIDE(Non-covalent)
SX.2: 6 residues within 4Å:- Chain A: Y.297, R.378, K.405, C.411
- Ligands: CU1.1, HEM.8
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.378, A:R.378, A:K.405
SX.29: 7 residues within 4Å:- Chain C: Y.297, Y.313, R.378, K.405, C.411
- Ligands: CU1.28, HEM.34
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:Y.297, C:Y.313, C:R.378, C:R.378, C:K.405
- 7 x BU3: (R,R)-2,3-BUTANEDIOL(Non-covalent)
BU3.3: 5 residues within 4Å:- Chain A: I.369, S.370, N.371
- Ligands: HEM.33, HEM.35
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:I.369
BU3.4: 5 residues within 4Å:- Chain A: K.300, S.406, Y.511, D.552, G.553
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:Y.511
- Hydrogen bonds: A:K.300, A:K.300
BU3.5: 2 residues within 4Å:- Chain A: G.427, T.432
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:T.432
BU3.17: 4 residues within 4Å:- Chain A: I.369
- Chain B: I.369, N.371
- Ligands: HEM.7
2 PLIP interactions:1 interactions with chain B, 1 interactions with chain A- Hydrophobic interactions: B:N.371, A:I.369
BU3.18: 5 residues within 4Å:- Chain B: K.300, S.406, Y.511, R.551, D.552
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:Y.511
- Hydrogen bonds: B:K.300, B:K.300
BU3.30: 5 residues within 4Å:- Chain C: I.369, S.370, N.371
- Ligands: HEM.20, HEM.22
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:I.369
BU3.31: 5 residues within 4Å:- Chain C: K.300, S.406, R.551, D.552, G.553
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:K.300, C:K.300
- 3 x ACT: ACETATE ION(Non-functional Binders)
ACT.6: 5 residues within 4Å:- Chain A: N.371, E.373, Q.377, G.415, Y.424
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:E.373
- Hydrogen bonds: A:Q.377, A:T.418
- Water bridges: A:Y.424
ACT.19: 6 residues within 4Å:- Chain B: N.371, E.373, Q.377, G.415, T.418, Y.424
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:E.373
- Hydrogen bonds: B:T.418
ACT.32: 6 residues within 4Å:- Chain C: N.371, E.373, Q.377, G.415, T.418, Y.424
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:E.373
- Water bridges: C:Y.424
- 24 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
HEM.7: 26 residues within 4Å:- Chain A: I.150, K.154, C.155, C.158, H.159, C.351, E.352, H.355, G.358, G.359, H.360, L.361, L.367
- Chain B: L.68, Y.71, R.136, V.137, A.138, I.369, S.370, N.371, C.372, E.373, R.374
- Ligands: HEM.9, BU3.17
17 PLIP interactions:10 interactions with chain B, 7 interactions with chain A,- Hydrophobic interactions: B:Y.71, B:R.136, B:A.138, B:E.373, B:R.374, A:I.150, A:E.352, A:H.355, A:L.361, A:L.367
- Hydrogen bonds: B:N.371, B:C.372, B:R.374
- Water bridges: B:I.369, B:I.369
- Metal complexes: A:H.159, A:H.360
HEM.8: 26 residues within 4Å:- Chain A: Y.135, R.170, V.214, G.215, H.216, R.218, T.219, K.220, F.221, F.224, R.230, Y.313, C.314, C.317, H.318, C.375, H.376, C.411, G.412, E.414, C.507, R.525
- Ligands: CU1.1, SX.2, HEM.10, HEM.11
19 PLIP interactions:19 interactions with chain A,- Hydrophobic interactions: A:V.214, A:K.220, A:F.224, A:R.230, A:Y.313, A:Y.313, A:Y.313
- Hydrogen bonds: A:H.216, A:T.219, A:K.220, A:K.220, A:G.412
- Salt bridges: A:H.216, A:H.376, A:R.525, A:R.525
- pi-Cation interactions: A:K.220, A:R.378
- Metal complexes: A:H.318
HEM.9: 22 residues within 4Å:- Chain A: C.155, H.159, Q.162, Y.163, W.166, H.171, V.349, S.350, C.351, C.354, H.355, I.369, S.370, A.431, P.436, H.437, K.471
- Chain B: N.371, E.373, R.429
- Ligands: HEM.7, HEM.10
14 PLIP interactions:10 interactions with chain A, 4 interactions with chain B,- Hydrophobic interactions: A:H.159, A:Q.162, A:Y.163, A:W.166, A:W.166, A:P.436
- Water bridges: A:K.471, B:R.429, B:R.429
- Salt bridges: A:K.471, B:R.429
- Metal complexes: A:H.355, A:H.437
- Hydrogen bonds: B:N.371
HEM.10: 25 residues within 4Å:- Chain A: R.170, H.171, T.174, H.216, V.316, C.317, H.318, V.349, C.354, S.370, C.372, R.374, C.375, H.376, C.430, H.434, P.436, V.439, T.440, S.466, P.468, R.525
- Ligands: HEM.8, HEM.9, HEM.11
17 PLIP interactions:17 interactions with chain A,- Hydrophobic interactions: A:V.349, A:H.434, A:P.436, A:V.439, A:V.439, A:V.439, A:P.468
- Hydrogen bonds: A:T.174, A:T.174, A:T.440, A:S.466, A:R.525
- Salt bridges: A:R.170, A:H.216, A:R.525
- Metal complexes: A:H.171, A:H.376
HEM.11: 24 residues within 4Å:- Chain A: R.218, H.376, E.414, G.415, T.418, H.423, M.428, R.429, C.430, C.433, H.434, S.466, K.467, P.468, L.470, M.501, F.503, R.525, R.526, H.528, W.530
- Ligands: HEM.8, HEM.10, HEM.12
19 PLIP interactions:19 interactions with chain A,- Hydrophobic interactions: A:H.376, A:E.414, A:E.414, A:P.468, A:L.470, A:R.526, A:W.530, A:W.530
- Hydrogen bonds: A:S.466
- Water bridges: A:S.466, A:S.466, A:R.526, A:R.526
- Salt bridges: A:R.218, A:K.467, A:R.525, A:R.526
- Metal complexes: A:H.434, A:H.528
HEM.12: 17 residues within 4Å:- Chain A: A.422, H.423, K.426, M.428, K.472, E.473, C.474, C.477, H.478, H.500, M.501, W.530, K.531, R.565
- Chain C: D.476
- Ligands: HEM.11, HEM.13
12 PLIP interactions:12 interactions with chain A,- Hydrophobic interactions: A:A.422, A:K.472, A:H.500
- Water bridges: A:A.422, A:K.531, A:R.565, A:R.565
- Salt bridges: A:K.426, A:K.531, A:R.565
- Metal complexes: A:H.423, A:H.478
HEM.13: 21 residues within 4Å:- Chain A: C.474, T.475, H.478, Q.481, A.482, Q.485, H.491, C.496, C.499, H.500, I.532, V.534, Q.618, D.669, G.670, S.671, W.672, M.674, H.675
- Ligands: HEM.12, HEM.14
16 PLIP interactions:16 interactions with chain A,- Hydrophobic interactions: A:T.475, A:H.478, A:Q.481, A:Q.485, A:H.491, A:I.532
- Hydrogen bonds: A:Q.618
- Water bridges: A:K.531, A:K.531, A:I.532, A:V.534, A:K.622
- Salt bridges: A:K.531, A:K.531
- Metal complexes: A:H.500, A:H.675
HEM.14: 20 residues within 4Å:- Chain A: T.490, H.491, N.494, S.498, C.499, A.573, C.574, R.576, A.587, K.588, C.590, H.591, L.598, L.602, F.604, E.613, V.614, W.617, M.674
- Ligands: HEM.13
10 PLIP interactions:10 interactions with chain A,- Hydrophobic interactions: A:A.587, A:K.588, A:L.598, A:L.602, A:F.604, A:V.614, A:W.617, A:W.617
- Metal complexes: A:H.491, A:H.591
HEM.20: 26 residues within 4Å:- Chain B: K.154, C.155, C.158, H.159, C.351, E.352, H.355, G.358, G.359, H.360, L.361, L.367
- Chain C: L.68, Y.71, R.136, V.137, A.138, L.368, I.369, S.370, N.371, C.372, E.373, R.374
- Ligands: HEM.22, BU3.30
16 PLIP interactions:10 interactions with chain C, 6 interactions with chain B,- Hydrophobic interactions: C:Y.71, C:R.136, C:A.138, C:E.373, C:R.374, B:E.352, B:H.355, B:L.361, B:L.361
- Hydrogen bonds: C:N.371, C:C.372, C:R.374
- Water bridges: C:I.369, C:I.369
- Metal complexes: B:H.159, B:H.360
HEM.21: 29 residues within 4Å:- Chain B: Y.135, R.170, V.214, G.215, H.216, R.218, T.219, K.220, F.221, G.222, F.224, R.230, Q.308, Y.313, C.314, C.317, H.318, C.375, H.376, R.378, C.411, G.412, E.414, C.507, R.525
- Ligands: CU1.15, SO2.16, HEM.23, HEM.24
19 PLIP interactions:19 interactions with chain B,- Hydrophobic interactions: B:V.214, B:K.220, B:F.224, B:R.230, B:Y.313, B:Y.313, B:Y.313
- Hydrogen bonds: B:H.216, B:T.219, B:K.220, B:K.220, B:G.412
- Salt bridges: B:H.216, B:H.376, B:R.525, B:R.525
- pi-Cation interactions: B:K.220, B:R.378
- Metal complexes: B:H.318
HEM.22: 23 residues within 4Å:- Chain B: C.155, H.159, Q.162, Y.163, W.166, H.171, V.349, S.350, C.351, C.354, H.355, I.369, S.370, A.431, P.436, H.437, K.471
- Chain C: N.371, E.373, R.429
- Ligands: HEM.20, HEM.23, BU3.30
15 PLIP interactions:10 interactions with chain B, 5 interactions with chain C,- Hydrophobic interactions: B:H.159, B:Q.162, B:Y.163, B:W.166, B:W.166, B:V.349, B:P.436
- Salt bridges: B:K.471, C:R.429
- Metal complexes: B:H.355, B:H.437
- Hydrogen bonds: C:N.371
- Water bridges: C:Y.424, C:Y.424, C:R.429
HEM.23: 24 residues within 4Å:- Chain B: R.170, H.171, T.174, H.216, V.316, C.317, H.318, V.349, C.354, S.370, C.372, R.374, C.375, H.376, C.430, P.436, V.439, T.440, S.466, P.468, R.525
- Ligands: HEM.21, HEM.22, HEM.24
14 PLIP interactions:14 interactions with chain B,- Hydrophobic interactions: B:V.349, B:P.436, B:V.439, B:V.439, B:P.468
- Hydrogen bonds: B:T.174, B:T.440, B:S.466, B:R.525
- Salt bridges: B:R.170, B:H.216, B:R.525
- Metal complexes: B:H.171, B:H.376
HEM.24: 23 residues within 4Å:- Chain B: R.218, H.376, E.414, G.415, H.423, M.428, R.429, C.430, C.433, H.434, S.466, K.467, P.468, L.470, M.501, F.503, R.525, R.526, H.528, W.530
- Ligands: HEM.21, HEM.23, HEM.25
20 PLIP interactions:20 interactions with chain B,- Hydrophobic interactions: B:H.376, B:E.414, B:E.414, B:P.468, B:L.470, B:R.526, B:W.530, B:W.530
- Hydrogen bonds: B:S.466, B:S.466
- Water bridges: B:S.466, B:S.466, B:R.526, B:R.526
- Salt bridges: B:R.218, B:K.467, B:R.525, B:R.526
- Metal complexes: B:H.434, B:H.528
HEM.25: 16 residues within 4Å:- Chain B: A.422, H.423, K.426, M.428, K.472, E.473, C.474, C.477, H.478, H.500, M.501, W.530, K.531, R.565
- Ligands: HEM.24, HEM.26
11 PLIP interactions:11 interactions with chain B,- Hydrophobic interactions: B:A.422, B:K.472, B:H.500
- Water bridges: B:K.531, B:K.531, B:R.565, B:R.565
- Salt bridges: B:K.531, B:R.565
- Metal complexes: B:H.423, B:H.478
HEM.26: 21 residues within 4Å:- Chain B: C.474, T.475, H.478, Q.481, A.482, Q.485, H.491, C.496, C.499, H.500, I.532, V.534, Q.618, D.669, G.670, S.671, W.672, M.674, H.675
- Ligands: HEM.25, HEM.27
15 PLIP interactions:15 interactions with chain B,- Hydrophobic interactions: B:T.475, B:H.478, B:Q.481, B:Q.481, B:H.491, B:I.532
- Hydrogen bonds: B:Q.618
- Water bridges: B:Q.481, B:I.532, B:V.534, B:E.667
- Salt bridges: B:K.531, B:K.531
- Metal complexes: B:H.500, B:H.675
HEM.27: 21 residues within 4Å:- Chain B: T.490, H.491, N.494, S.498, C.499, L.570, A.573, C.574, R.576, A.587, C.590, H.591, L.598, L.602, F.604, V.610, E.613, V.614, W.617, M.674
- Ligands: HEM.26
11 PLIP interactions:11 interactions with chain B,- Hydrophobic interactions: B:L.570, B:A.587, B:L.598, B:L.598, B:L.602, B:F.604, B:V.610, B:V.614, B:W.617
- Metal complexes: B:H.491, B:H.591
HEM.33: 26 residues within 4Å:- Chain A: L.68, Y.71, R.136, V.137, A.138, L.368, I.369, S.370, N.371, C.372, E.373, R.374
- Chain C: I.150, K.154, C.155, C.158, H.159, C.351, H.355, G.358, G.359, H.360, L.361, L.367
- Ligands: BU3.3, HEM.35
18 PLIP interactions:6 interactions with chain C, 12 interactions with chain A,- Hydrophobic interactions: C:I.150, C:H.355, C:L.361, C:L.367, A:Y.71, A:R.136, A:A.138, A:E.373, A:R.374
- Metal complexes: C:H.159, C:H.360
- Hydrogen bonds: A:N.371, A:N.371, A:C.372, A:E.373, A:R.374
- Water bridges: A:I.369, A:I.369
HEM.34: 29 residues within 4Å:- Chain C: Y.135, R.170, V.214, G.215, H.216, R.218, T.219, K.220, F.221, G.222, F.224, R.230, Q.308, Y.313, C.314, C.317, H.318, R.374, C.375, H.376, C.411, G.412, E.414, C.507, R.525
- Ligands: CU1.28, SX.29, HEM.36, HEM.37
20 PLIP interactions:20 interactions with chain C,- Hydrophobic interactions: C:V.214, C:K.220, C:F.224, C:R.230, C:Y.313, C:Y.313, C:Y.313
- Hydrogen bonds: C:H.216, C:T.219, C:T.219, C:K.220, C:K.220, C:G.412
- Salt bridges: C:H.216, C:H.376, C:R.525, C:R.525
- pi-Cation interactions: C:K.220, C:R.378
- Metal complexes: C:H.318
HEM.35: 23 residues within 4Å:- Chain A: N.371, E.373, R.429
- Chain C: C.155, H.159, Q.162, Y.163, W.166, H.171, V.349, S.350, C.351, C.354, H.355, I.369, S.370, A.431, P.436, H.437, K.471
- Ligands: BU3.3, HEM.33, HEM.36
16 PLIP interactions:4 interactions with chain A, 12 interactions with chain C,- Hydrogen bonds: A:N.371
- Water bridges: A:R.429, A:R.429, C:Q.162, C:K.471
- Salt bridges: A:R.429, C:K.471
- Hydrophobic interactions: C:H.159, C:Y.163, C:W.166, C:W.166, C:V.349, C:I.369, C:P.436
- Metal complexes: C:H.355, C:H.437
HEM.36: 23 residues within 4Å:- Chain C: R.170, H.171, T.174, H.216, V.316, C.317, H.318, V.349, C.354, S.370, C.372, R.374, C.375, H.376, C.430, V.439, T.440, S.466, P.468, R.525
- Ligands: HEM.34, HEM.35, HEM.37
14 PLIP interactions:14 interactions with chain C,- Hydrophobic interactions: C:V.349, C:V.439, C:V.439, C:P.468
- Hydrogen bonds: C:T.174, C:T.174, C:T.440, C:S.466, C:R.525
- Salt bridges: C:R.170, C:H.216, C:R.525
- Metal complexes: C:H.171, C:H.376
HEM.37: 23 residues within 4Å:- Chain C: R.218, H.376, E.414, G.415, H.423, M.428, R.429, C.430, C.433, H.434, S.466, K.467, P.468, L.470, M.501, F.503, R.525, R.526, H.528, W.530
- Ligands: HEM.34, HEM.36, HEM.38
21 PLIP interactions:21 interactions with chain C,- Hydrophobic interactions: C:H.376, C:E.414, C:E.414, C:P.468, C:L.470, C:R.526, C:W.530, C:W.530
- Hydrogen bonds: C:S.466
- Water bridges: C:R.218, C:S.466, C:S.466, C:K.467, C:R.526, C:R.526
- Salt bridges: C:R.218, C:K.467, C:R.525, C:R.526
- Metal complexes: C:H.434, C:H.528
HEM.38: 17 residues within 4Å:- Chain B: D.476
- Chain C: A.422, H.423, K.426, M.428, K.472, E.473, C.474, C.477, H.478, H.500, M.501, W.530, K.531, R.565
- Ligands: HEM.37, HEM.39
16 PLIP interactions:16 interactions with chain C,- Hydrophobic interactions: C:K.426, C:K.472, C:K.472, C:H.500
- Water bridges: C:A.422, C:K.531, C:K.531, C:R.565, C:R.565, C:R.565, C:R.565
- Salt bridges: C:K.426, C:K.531, C:R.565
- Metal complexes: C:H.423, C:H.478
HEM.39: 21 residues within 4Å:- Chain C: C.474, T.475, H.478, Q.481, A.482, Q.485, H.491, S.495, C.496, C.499, H.500, I.532, V.534, Q.618, D.669, G.670, S.671, W.672, H.675
- Ligands: HEM.38, HEM.40
14 PLIP interactions:14 interactions with chain C,- Hydrophobic interactions: C:T.475, C:H.478, C:Q.481, C:Q.481, C:I.532
- Hydrogen bonds: C:Q.618
- Water bridges: C:K.531, C:K.531, C:K.531, C:I.532
- Salt bridges: C:K.531, C:K.531
- Metal complexes: C:H.500, C:H.675
HEM.40: 18 residues within 4Å:- Chain C: T.490, H.491, N.494, S.498, C.499, L.570, A.573, C.574, A.587, C.590, H.591, L.598, L.602, E.613, V.614, W.617, M.674
- Ligands: HEM.39
9 PLIP interactions:9 interactions with chain C,- Hydrophobic interactions: C:L.570, C:A.587, C:L.598, C:L.602, C:V.614, C:W.617, C:W.617
- Metal complexes: C:H.491, C:H.591
- 1 x SO2: SULFUR DIOXIDE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Hermann, B. et al., The octahaem MccA is a haem c-copper sulfite reductase. Nature (2015)
- Release Date
- 2015-02-04
- Peptides
- MccA: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
FB
IC
J
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- homo-trimer
- Ligands
- 3 x CU1: COPPER (I) ION(Non-covalent)
- 2 x SX: SULFUR OXIDE(Non-covalent)
- 7 x BU3: (R,R)-2,3-BUTANEDIOL(Non-covalent)
- 3 x ACT: ACETATE ION(Non-functional Binders)
- 24 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 1 x SO2: SULFUR DIOXIDE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Hermann, B. et al., The octahaem MccA is a haem c-copper sulfite reductase. Nature (2015)
- Release Date
- 2015-02-04
- Peptides
- MccA: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
FB
IC
J