SMTL ID : 9nsj.1

Finding the exit route of hydrogen peroxide from the manganese superoxide dismutase (MnSOD) active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.33 Å

Oligo State

homo-dimer

Ligands

101 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)

PEO.1: 6 residues within 4Å: Chain A: Q.62, P.63, K.66 Chain B: Q.62 Ligands: PEO.58, PEO.67 Ligand excluded by PLIP PEO.2: 4 residues within 4Å: Chain A: N.38, A.64, F.67, N.68 Ligand excluded by PLIP PEO.7: 10 residues within 4Å: Chain A: H.27, Y.35, H.75, W.124, N.144, D.160, W.162, H.164 Ligands: PEO.11, MN.66 Ligand excluded by PLIP PEO.8: 5 residues within 4Å: Chain A: P.17, H.18, N.183 Ligands: PEO.34, PEO.51 Ligand excluded by PLIP PEO.9: 5 residues within 4Å: Chain A: G.87, E.89, P.90, W.187, E.188 Ligand excluded by PLIP PEO.10: 3 residues within 4Å: Chain A: Q.25, S.29, K.30 Ligand excluded by PLIP PEO.11: 5 residues within 4Å: Chain A: H.31, Y.35, W.162, H.164 Ligands: PEO.7 Ligand excluded by PLIP PEO.12: 5 residues within 4Å: Chain A: A.139, A.140, C.141, P.142, T.151 Ligand excluded by PLIP PEO.13: 5 residues within 4Å: Chain A: K.2, N.40, E.43, E.44 Ligands: PEO.35 Ligand excluded by PLIP PEO.14: 6 residues within 4Å: Chain A: N.37, N.38, V.41 Ligands: PEO.23, PEO.56, PEO.57 Ligand excluded by PLIP PEO.15: 6 residues within 4Å: Chain A: L.5, P.6, D.7, H.28 Ligands: PEO.40, PEO.54 Ligand excluded by PLIP PEO.16: 5 residues within 4Å: Chain A: G.53, D.54, V.55 Ligands: PEO.55, PEO.59 Ligand excluded by PLIP PEO.17: 8 residues within 4Å: Chain A: H.72, I.73, S.76 Ligands: PO4.6, PEO.49, PEO.53, PEO.95, PEO.125 Ligand excluded by PLIP PEO.18: 6 residues within 4Å: Chain A: N.38, V.41, T.42, K.45, L.61, A.64 Ligand excluded by PLIP PEO.19: 5 residues within 4Å: Chain A: Q.169, Y.170, K.171, V.173, D.176 Ligand excluded by PLIP PEO.20: 6 residues within 4Å: Chain A: G.88, E.89, F.105, K.109, W.182, W.187 Ligand excluded by PLIP PEO.21: 5 residues within 4Å: Chain A: P.17, H.18 Ligands: K.27, PEO.63, PEO.65 Ligand excluded by PLIP PEO.22: 6 residues within 4Å: Chain A: K.2, H.3, S.4, V.36, N.40 Ligands: PEO.46 Ligand excluded by PLIP PEO.23: 5 residues within 4Å: Chain A: A.33, A.34, N.37 Ligands: PEO.14, PEO.57 Ligand excluded by PLIP PEO.24: 4 residues within 4Å: Chain A: Y.12, A.21, Q.22, Q.25 Ligand excluded by PLIP PEO.33: 4 residues within 4Å: Chain A: E.16, P.17, N.20, Q.169 Ligand excluded by PLIP PEO.34: 5 residues within 4Å: Chain A: H.18, G.86, G.87, N.183 Ligands: PEO.8 Ligand excluded by PLIP PEO.35: 7 residues within 4Å: Chain A: M.1, K.2, H.3, N.40, E.43 Ligands: PEO.13, PEO.61 Ligand excluded by PLIP PEO.36: 5 residues within 4Å: Chain A: T.113, P.175, D.176, L.178, K.179 Ligand excluded by PLIP PEO.37: 3 residues within 4Å: Chain A: G.118, V.119, Q.120 Ligand excluded by PLIP PEO.38: 3 residues within 4Å: Chain A: G.103, S.104, K.107 Ligand excluded by PLIP PEO.39: 3 residues within 4Å: Chain A: I.77, R.193 Ligands: PEO.49 Ligand excluded by PLIP PEO.40: 5 residues within 4Å: Chain A: L.5, Y.12, H.28, S.29 Ligands: PEO.15 Ligand excluded by PLIP PEO.41: 5 residues within 4Å: Chain A: K.131, Q.148, G.152, I.154 Ligands: PEO.43 Ligand excluded by PLIP PEO.42: 5 residues within 4Å: Chain A: L.8, Y.10, D.11, Y.12 Ligands: PEO.47 Ligand excluded by PLIP PEO.43: 8 residues within 4Å: Chain A: F.129, N.130, K.131, E.132, G.152, L.153, I.154 Ligands: PEO.41 Ligand excluded by PLIP PEO.44: 4 residues within 4Å: Chain A: A.60, P.63 Chain B: G.149 Ligands: PEO.67 Ligand excluded by PLIP PEO.45: 9 residues within 4Å: Chain A: P.90, K.91, G.92, E.93, L.94, L.95, T.191, Y.194, M.195 Ligand excluded by PLIP PEO.46: 3 residues within 4Å: Chain A: S.4 Ligands: PEO.22, PEO.54 Ligand excluded by PLIP PEO.47: 5 residues within 4Å: Chain A: D.7, L.8, P.9 Ligands: PEO.42, PEO.48 Ligand excluded by PLIP PEO.48: 2 residues within 4Å: Chain A: D.7 Ligands: PEO.47 Ligand excluded by PLIP PEO.49: 6 residues within 4Å: Chain A: S.76 Ligands: PO4.6, PEO.17, PEO.39, PEO.50, PEO.53 Ligand excluded by PLIP PEO.50: 4 residues within 4Å: Ligands: PO4.6, K.26, PEO.49, PEO.53 Ligand excluded by PLIP PEO.51: 8 residues within 4Å: Chain A: A.14, L.15, E.16, P.17, H.18, P.84, V.184 Ligands: PEO.8 Ligand excluded by PLIP PEO.52: 1 residues within 4Å: Chain A: Q.148 Ligand excluded by PLIP PEO.53: 9 residues within 4Å: Chain A: S.4, P.6, H.72, S.76 Ligands: PO4.6, PEO.17, K.26, PEO.49, PEO.50 Ligand excluded by PLIP PEO.54: 6 residues within 4Å: Chain A: S.4, L.5, P.6, D.7 Ligands: PEO.15, PEO.46 Ligand excluded by PLIP PEO.55: 7 residues within 4Å: Chain A: D.54, V.55, T.56 Chain B: I.73 Ligands: PEO.16, PEO.59, PEO.93 Ligand excluded by PLIP PEO.56: 4 residues within 4Å: Chain A: A.34, N.38 Ligands: PEO.14, PEO.57 Ligand excluded by PLIP PEO.57: 6 residues within 4Å: Chain A: A.34, N.37, N.38 Ligands: PEO.14, PEO.23, PEO.56 Ligand excluded by PLIP PEO.58: 5 residues within 4Å: Chain A: Q.62 Chain B: Q.62, P.63, K.66 Ligands: PEO.1 Ligand excluded by PLIP PEO.59: 9 residues within 4Å: Chain A: V.55 Chain B: H.3, L.39, H.72, I.73 Ligands: PEO.16, PEO.55, PO4.68, PEO.93 Ligand excluded by PLIP PEO.60: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PEO.61: 7 residues within 4Å: Chain A: M.1, K.2, H.3, N.40, E.43 Chain B: G.53 Ligands: PEO.35 Ligand excluded by PLIP PEO.62: 4 residues within 4Å: Chain A: K.2, H.3, S.4 Ligands: PO4.6 Ligand excluded by PLIP PEO.63: 10 residues within 4Å: Chain A: P.17, H.18, Q.169, Y.170, A.180 Ligands: PEO.21, K.27, K.29, PEO.64, PEO.65 Ligand excluded by PLIP PEO.64: 7 residues within 4Å: Chain A: Y.170, D.176, K.179, A.180 Ligands: K.27, K.29, PEO.63 Ligand excluded by PLIP PEO.65: 8 residues within 4Å: Chain A: P.17, H.18, Y.170, A.180, N.183 Ligands: PEO.21, K.27, PEO.63 Ligand excluded by PLIP PEO.67: 9 residues within 4Å: Chain A: I.59, A.60, Q.62, P.63 Chain B: K.66, G.149, T.150 Ligands: PEO.1, PEO.44 Ligand excluded by PLIP PEO.69: 3 residues within 4Å: Chain B: D.11, A.14, P.84 Ligand excluded by PLIP PEO.70: 8 residues within 4Å: Chain A: K.66, G.149, T.150 Chain B: I.59, A.60, Q.62, P.63 Ligands: PEO.113 Ligand excluded by PLIP PEO.72: 5 residues within 4Å: Chain B: Y.170, K.171, V.173, D.176 Ligands: PEO.116 Ligand excluded by PLIP PEO.75: 3 residues within 4Å: Chain B: P.142, N.143 Ligands: PO4.107 Ligand excluded by PLIP PEO.76: 5 residues within 4Å: Chain B: T.80, N.189, R.193 Ligands: PEO.84, PEO.108 Ligand excluded by PLIP PEO.78: 4 residues within 4Å: Chain B: E.16, P.17, N.20, Q.169 Ligand excluded by PLIP PEO.79: 3 residues within 4Å: Chain B: G.118, V.119, A.140 Ligand excluded by PLIP PEO.80: 8 residues within 4Å: Chain B: K.30, H.31, A.34 Ligands: PEO.81, PEO.99, PEO.115, PEO.117, PEO.121 Ligand excluded by PLIP PEO.81: 7 residues within 4Å: Chain B: H.31 Ligands: PEO.80, PEO.85, PEO.99, PEO.115, PEO.117, PEO.121 Ligand excluded by PLIP PEO.82: 11 residues within 4Å: Chain B: H.27, H.31, Y.35, H.75, W.124, N.144, D.160, W.162, H.164 Ligands: PEO.99, MN.127 Ligand excluded by PLIP PEO.83: 8 residues within 4Å: Chain B: F.129, N.130, K.131, E.132, G.152, L.153, I.154 Ligands: PO4.77 Ligand excluded by PLIP PEO.84: 5 residues within 4Å: Chain B: I.77, R.193 Ligands: PEO.76, PEO.108, PEO.109 Ligand excluded by PLIP PEO.85: 5 residues within 4Å: Chain B: F.67, W.162 Ligands: PEO.81, PEO.115, PEO.121 Ligand excluded by PLIP PEO.86: 3 residues within 4Å: Chain B: Q.169, K.171 Ligands: PEO.116 Ligand excluded by PLIP PEO.87: 5 residues within 4Å: Chain B: N.38, A.64, F.67, N.68 Ligands: PEO.117 Ligand excluded by PLIP PEO.88: 6 residues within 4Å: Chain B: L.5, A.33, V.36, N.37 Ligands: PEO.89, PEO.94 Ligand excluded by PLIP PEO.89: 6 residues within 4Å: Chain B: L.5, A.33, N.37 Ligands: PEO.88, PEO.90, PEO.98 Ligand excluded by PLIP PEO.90: 6 residues within 4Å: Chain B: L.5, S.29, A.33 Ligands: PEO.89, PEO.98, PEO.114 Ligand excluded by PLIP PEO.91: 6 residues within 4Å: Chain B: A.140, C.141, P.142, D.145, T.150, T.151 Ligand excluded by PLIP PEO.92: 3 residues within 4Å: Chain B: K.52 Ligands: PO4.6, PEO.95 Ligand excluded by PLIP PEO.93: 6 residues within 4Å: Chain B: H.72, I.73, S.76 Ligands: PEO.55, PEO.59, K.104 Ligand excluded by PLIP PEO.94: 6 residues within 4Å: Chain B: H.3, S.4, L.5, V.36 Ligands: PEO.88, PEO.114 Ligand excluded by PLIP PEO.95: 7 residues within 4Å: Chain B: K.52, G.53, D.54 Ligands: PO4.6, PEO.17, PEO.92, PEO.125 Ligand excluded by PLIP PEO.96: 2 residues within 4Å: Chain B: K.30 Ligands: PEO.100 Ligand excluded by PLIP PEO.97: 2 residues within 4Å: Chain B: K.179, N.183 Ligand excluded by PLIP PEO.98: 7 residues within 4Å: Chain B: L.5, Y.12, H.28, S.29 Ligands: PEO.89, PEO.90, PEO.114 Ligand excluded by PLIP PEO.99: 9 residues within 4Å: Chain B: H.31, Y.35, W.162, H.164 Ligands: PEO.80, PEO.81, PEO.82, PEO.115, PEO.117 Ligand excluded by PLIP PEO.100: 3 residues within 4Å: Chain B: K.30, A.34 Ligands: PEO.96 Ligand excluded by PLIP PEO.108: 6 residues within 4Å: Chain B: T.80, N.189, R.193 Ligands: PEO.76, PEO.84, PEO.111 Ligand excluded by PLIP PEO.109: 7 residues within 4Å: Chain B: I.77, Q.148, I.154, P.155, R.193 Ligands: PEO.84, PEO.112 Ligand excluded by PLIP PEO.110: 7 residues within 4Å: Chain A: T.56, A.60 Chain B: Q.148, G.149, T.150, T.151, G.152 Ligand excluded by PLIP PEO.111: 5 residues within 4Å: Chain B: P.6, S.76, T.80 Ligands: K.104, PEO.108 Ligand excluded by PLIP PEO.112: 4 residues within 4Å: Chain B: I.154, A.196, C.197 Ligands: PEO.109 Ligand excluded by PLIP PEO.113: 4 residues within 4Å: Chain A: G.149 Chain B: A.60, P.63 Ligands: PEO.70 Ligand excluded by PLIP PEO.114: 6 residues within 4Å: Chain B: L.5, D.7, H.28 Ligands: PEO.90, PEO.94, PEO.98 Ligand excluded by PLIP PEO.115: 11 residues within 4Å: Chain B: H.31, Y.35, F.67, W.162, H.164 Ligands: PEO.80, PEO.81, PEO.85, PEO.99, PEO.117, PEO.121 Ligand excluded by PLIP PEO.116: 4 residues within 4Å: Chain B: Q.169, Y.170 Ligands: PEO.72, PEO.86 Ligand excluded by PLIP PEO.117: 10 residues within 4Å: Chain B: A.34, Y.35, N.38, F.67 Ligands: PEO.80, PEO.81, PEO.87, PEO.99, PEO.115, PEO.121 Ligand excluded by PLIP PEO.118: 4 residues within 4Å: Chain B: K.109, T.113, K.179, W.182 Ligand excluded by PLIP PEO.119: 9 residues within 4Å: Chain B: P.90, K.91, G.92, E.93, L.94, L.95, T.191, Y.194, M.195 Ligand excluded by PLIP PEO.120: 2 residues within 4Å: Chain B: K.2, N.40 Ligand excluded by PLIP PEO.121: 6 residues within 4Å: Chain B: F.67 Ligands: PEO.80, PEO.81, PEO.85, PEO.115, PEO.117 Ligand excluded by PLIP PEO.122: 3 residues within 4Å: Chain B: D.7, L.8, P.9 Ligand excluded by PLIP PEO.123: 4 residues within 4Å: Chain B: L.5, P.6, D.7 Ligands: PEO.124 Ligand excluded by PLIP PEO.124: 4 residues within 4Å: Chain B: S.4, L.5, P.6 Ligands: PEO.123 Ligand excluded by PLIP PEO.125: 9 residues within 4Å: Chain A: H.3, I.73 Chain B: G.53, D.54, V.55, T.56 Ligands: PO4.6, PEO.17, PEO.95 Ligand excluded by PLIP PEO.126: 3 residues within 4Å: Chain B: V.173, P.175, D.176 Ligand excluded by PLIP

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

PO4.3: 1 residues within 4Å: Chain A: K.171 8 PLIP interactions: 8 interactions with chain A Water bridges: A:L.168, A:L.168, A:K.171, A:K.171, A:K.171, A:K.171, A:K.171 Salt bridges: A:K.171 PO4.4: 3 residues within 4Å: Chain A: K.66, N.143 Ligands: PO4.107 7 PLIP interactions: 7 interactions with chain A Water bridges: A:K.66, A:K.66, A:K.66, A:K.66, A:N.143, A:N.143 Salt bridges: A:K.66 PO4.5: 1 residues within 4Å: Chain A: K.30 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.30 PO4.6: 14 residues within 4Å: Chain A: H.3, S.4, H.72, S.76 Chain B: G.53 Ligands: PEO.17, K.26, PEO.49, PEO.50, PEO.53, PEO.62, PEO.92, PEO.95, PEO.125 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.3, A:H.72 PO4.32: 1 residues within 4Å: Chain A: K.99 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.99, A:K.99 Salt bridges: A:K.99 PO4.68: 5 residues within 4Å: Chain B: H.3, S.4, H.72 Ligands: PEO.59, K.104 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.4 Salt bridges: B:H.3, B:H.72 PO4.71: 1 residues within 4Å: Chain B: K.171 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.171, B:K.171 Salt bridges: B:K.171 PO4.73: 3 residues within 4Å: Chain B: S.104, D.106, K.107 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.104, B:S.104, B:S.104, B:D.106 PO4.74: 2 residues within 4Å: Chain B: L.95, K.99 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.99, B:K.99 Salt bridges: B:K.99 PO4.77: 2 residues within 4Å: Chain B: E.132 Ligands: PEO.83 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.132, B:E.132 Water bridges: B:N.130, B:E.132 PO4.107: 4 residues within 4Å: Chain B: K.66, N.143 Ligands: PO4.4, PEO.75 7 PLIP interactions: 7 interactions with chain B Water bridges: B:K.66, B:K.66, B:K.66, B:K.66, B:N.143, B:D.145 Salt bridges: B:K.66

13 x K: POTASSIUM ION(Non-covalent)

K.25: 5 residues within 4Å: Chain A: K.66, F.67, N.143, N.144, D.145 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.145, H2O.11 K.26: 6 residues within 4Å: Chain A: S.4, P.6, H.72 Ligands: PO4.6, PEO.50, PEO.53 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.4, H2O.1 K.27: 8 residues within 4Å: Chain A: K.179, A.180, N.183 Ligands: PEO.21, K.29, PEO.63, PEO.64, PEO.65 No protein-ligand interaction detected (PLIP) K.28: 3 residues within 4Å: Chain A: I.154, P.155, R.193 No protein-ligand interaction detected (PLIP) K.29: 4 residues within 4Å: Chain A: Y.170 Ligands: K.27, PEO.63, PEO.64 No protein-ligand interaction detected (PLIP) K.30: 6 residues within 4Å: Chain A: I.19, I.23, H.27, F.78, A.165, Y.177 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.165, H2O.5 K.31: 2 residues within 4Å: Chain A: G.13, E.16 No protein-ligand interaction detected (PLIP) K.101: 9 residues within 4Å: Chain B: Y.12, G.13, A.14, L.15, E.16, I.19, N.20, A.21, M.24 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:Y.12, B:I.19 K.102: 5 residues within 4Å: Chain B: K.66, F.67, N.143, N.144, D.145 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.145, H2O.25 K.103: 3 residues within 4Å: Chain B: K.99, R.100, G.103 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:K.99, B:G.103, H2O.22, H2O.22, H2O.24 K.104: 6 residues within 4Å: Chain B: P.6, H.72, S.76 Ligands: PO4.68, PEO.93, PEO.111 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.76, H2O.18 K.105: 6 residues within 4Å: Chain B: I.19, I.23, H.27, F.78, A.165, Y.177 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.165, B:Y.177, H2O.19 K.106: 5 residues within 4Å: Chain B: P.17, H.18, Q.169, Y.170, A.180 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:Y.170, H2O.17, H2O.26

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.66: 7 residues within 4Å: Chain A: H.27, H.75, W.124, D.160, W.162, H.164 Ligands: PEO.7 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.27, A:H.75, A:D.160, A:H.164, H2O.1 MN.127: 8 residues within 4Å: Chain B: H.27, Y.35, H.75, W.124, D.160, W.162, H.164 Ligands: PEO.82 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.27, B:H.75, B:D.160, B:H.164, H2O.14

Links

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Citation

Dasgupta, M. et al., Mapping the Exit Route of Hydrogen Peroxide From the Manganese Superoxide Dismutase (MnSOD) Active Site. Biorxiv (2025)

Release Date

2025-08-27

Peptides

Superoxide dismutase [Mn], mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Superoxide dismutase [Mn], mitochondrial

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