SMTL ID : 2ymw.1

Structure of the epsilon-lysine oxidase from Marinomonas mediterranea

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: D.270, A.272, I.275, P.603, Q.604 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.275 NA.2: 6 residues within 4Å: Chain A: C.536, T.537, W.600, W.601, P.602, S.605 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.537, A:W.600 NA.46: 5 residues within 4Å: Chain B: D.270, A.272, I.275, P.603, Q.604 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.275 NA.47: 6 residues within 4Å: Chain B: C.536, T.537, W.600, W.601, P.602, S.605 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.600, B:S.605 NA.78: 5 residues within 4Å: Chain C: D.270, A.272, I.275, P.603, Q.604 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.272 NA.79: 6 residues within 4Å: Chain C: C.536, T.537, W.600, W.601, P.602, S.605 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:W.600, C:S.605 NA.123: 5 residues within 4Å: Chain D: D.270, A.272, I.275, P.603, Q.604 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.270 NA.124: 6 residues within 4Å: Chain D: C.536, T.537, W.600, W.601, P.602, S.605 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.537, D:W.600

142 x EOH: ETHANOL(Non-functional Binders)

EOH.3: 8 residues within 4Å: Chain A: N.334, V.335, M.399, Y.596, Y.597, Y.599 Chain C: G.627 Ligands: EOH.5 Ligand excluded by PLIP EOH.4: 1 residues within 4Å: Chain A: K.372 Ligand excluded by PLIP EOH.5: 7 residues within 4Å: Chain A: N.334, Y.597, Y.599 Chain C: G.627, Q.628, Q.629 Ligands: EOH.3 Ligand excluded by PLIP EOH.6: 1 residues within 4Å: Chain A: D.378 Ligand excluded by PLIP EOH.7: 1 residues within 4Å: Chain A: D.131 Ligand excluded by PLIP EOH.8: 3 residues within 4Å: Chain A: M.360, K.361, N.364 Ligand excluded by PLIP EOH.9: 7 residues within 4Å: Chain A: H.621, H.623, H.672, E.673, F.675, D.676, K.705 Ligand excluded by PLIP EOH.10: 6 residues within 4Å: Chain A: K.113, I.241, I.471, M.525, W.529, D.532 Ligand excluded by PLIP EOH.11: 4 residues within 4Å: Chain A: S.343 Chain C: Q.324, F.342, F.344 Ligand excluded by PLIP EOH.12: 4 residues within 4Å: Chain A: N.41, N.68, K.70, R.77 Ligand excluded by PLIP EOH.13: 2 residues within 4Å: Chain A: A.353, A.354 Ligand excluded by PLIP EOH.14: 6 residues within 4Å: Chain A: Q.382, V.383, L.384, M.385, F.543 Ligands: EOH.23 Ligand excluded by PLIP EOH.15: 3 residues within 4Å: Chain A: N.90, V.451, S.452 Ligand excluded by PLIP EOH.16: 3 residues within 4Å: Chain A: W.607, N.631, A.633 Ligand excluded by PLIP EOH.17: 5 residues within 4Å: Chain A: Y.377, T.415, S.547 Chain D: A.570 Ligands: EOH.30 Ligand excluded by PLIP EOH.18: 5 residues within 4Å: Chain A: D.40, N.41, F.42, H.56, R.77 Ligand excluded by PLIP EOH.19: 3 residues within 4Å: Chain A: A.526, D.532 Ligands: EOH.39 Ligand excluded by PLIP EOH.20: 1 residues within 4Å: Chain A: S.154 Ligand excluded by PLIP EOH.21: 4 residues within 4Å: Chain A: S.189, L.192, N.225, D.236 Ligand excluded by PLIP EOH.22: 2 residues within 4Å: Chain A: D.347 Ligands: EOH.99 Ligand excluded by PLIP EOH.23: 3 residues within 4Å: Chain A: E.388, S.544 Ligands: EOH.14 Ligand excluded by PLIP EOH.24: 3 residues within 4Å: Chain A: Y.492, Y.497, T.504 Ligand excluded by PLIP EOH.25: 5 residues within 4Å: Chain A: F.366, R.367, Q.368, P.380, L.396 Ligand excluded by PLIP EOH.26: 7 residues within 4Å: Chain A: S.622, L.624, R.634, R.670, H.672, F.675, F.699 Ligand excluded by PLIP EOH.27: 4 residues within 4Å: Chain A: P.569, A.570 Chain D: S.409, S.547 Ligand excluded by PLIP EOH.28: 4 residues within 4Å: Chain A: Q.657, N.658, N.659, D.660 Ligand excluded by PLIP EOH.29: 2 residues within 4Å: Chain A: I.49, G.50 Ligand excluded by PLIP EOH.30: 6 residues within 4Å: Chain A: S.409, N.410, T.415 Chain D: P.569, A.570 Ligands: EOH.17 Ligand excluded by PLIP EOH.31: 3 residues within 4Å: Chain A: Q.324, G.661 Chain C: Q.345 Ligand excluded by PLIP EOH.32: 3 residues within 4Å: Chain A: Y.54, P.62, T.63 Ligand excluded by PLIP EOH.33: 3 residues within 4Å: Chain A: K.550, K.589, P.591 Ligand excluded by PLIP EOH.34: 6 residues within 4Å: Chain A: V.31, N.45, P.46, Q.81, A.457, S.458 Ligand excluded by PLIP EOH.35: 3 residues within 4Å: Chain A: G.129, R.130, D.131 Ligand excluded by PLIP EOH.36: 5 residues within 4Å: Chain A: I.178, P.179, E.180, Y.182, P.185 Ligand excluded by PLIP EOH.37: 3 residues within 4Å: Chain A: N.371, D.376, D.378 Ligand excluded by PLIP EOH.38: 3 residues within 4Å: Chain A: D.301, A.303, T.304 Ligand excluded by PLIP EOH.39: 4 residues within 4Å: Chain A: E.118, A.526, C.527 Ligands: EOH.19 Ligand excluded by PLIP EOH.40: 3 residues within 4Å: Chain A: Q.153, L.183, H.184 Ligand excluded by PLIP EOH.41: 2 residues within 4Å: Chain A: A.144, S.145 Ligand excluded by PLIP EOH.42: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EOH.43: 1 residues within 4Å: Chain D: Q.553 Ligand excluded by PLIP EOH.44: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EOH.45: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EOH.48: 3 residues within 4Å: Chain B: G.195, K.197 Ligands: GOL.73 Ligand excluded by PLIP EOH.49: 4 residues within 4Å: Chain B: G.74, E.669, N.671 Ligands: EOH.50 Ligand excluded by PLIP EOH.50: 5 residues within 4Å: Chain B: E.613, E.669, R.670, H.672 Ligands: EOH.49 Ligand excluded by PLIP EOH.51: 2 residues within 4Å: Chain B: Q.368, P.380 Ligand excluded by PLIP EOH.52: 3 residues within 4Å: Chain B: H.623, D.676, F.677 Ligand excluded by PLIP EOH.53: 3 residues within 4Å: Chain B: S.695 Ligands: EOH.60, EOH.61 Ligand excluded by PLIP EOH.54: 4 residues within 4Å: Chain A: H.621, E.673 Chain B: S.579, V.580 Ligand excluded by PLIP EOH.55: 4 residues within 4Å: Chain B: R.349, G.351, F.441, A.443 Ligand excluded by PLIP EOH.56: 5 residues within 4Å: Chain B: G.50, G.51, L.52, E.274, Q.657 Ligand excluded by PLIP EOH.57: 3 residues within 4Å: Chain B: V.383, L.384, F.543 Ligand excluded by PLIP EOH.58: 2 residues within 4Å: Chain B: D.448, D.453 Ligand excluded by PLIP EOH.59: 4 residues within 4Å: Chain B: E.48, I.49, D.453, T.456 Ligand excluded by PLIP EOH.60: 3 residues within 4Å: Chain B: P.697 Ligands: EOH.53, EOH.61 Ligand excluded by PLIP EOH.61: 6 residues within 4Å: Chain B: F.677, E.679, S.695, P.697 Ligands: EOH.53, EOH.60 Ligand excluded by PLIP EOH.62: 8 residues within 4Å: Chain B: N.334, V.335, M.399, Y.596, Y.597, S.598, Y.599 Chain D: G.627 Ligand excluded by PLIP EOH.63: 9 residues within 4Å: Chain B: K.113, I.241, V.266, G.267, S.268, I.471, E.472, T.522, M.525 Ligand excluded by PLIP EOH.64: 5 residues within 4Å: Chain B: N.125, Y.128, K.372, E.420, Q.478 Ligand excluded by PLIP EOH.65: 3 residues within 4Å: Chain B: Y.363, G.434, E.438 Ligand excluded by PLIP EOH.66: 3 residues within 4Å: Chain B: G.351, S.352, A.353 Ligand excluded by PLIP EOH.67: 3 residues within 4Å: Chain B: V.171, N.177 Ligands: EOH.75 Ligand excluded by PLIP EOH.68: 8 residues within 4Å: Chain B: S.196, G.220, F.221, A.222, Q.530, V.643, E.644, W.646 Ligand excluded by PLIP EOH.69: 1 residues within 4Å: Chain B: G.375 Ligand excluded by PLIP EOH.70: 3 residues within 4Å: Chain A: E.617 Chain B: Q.577, S.578 Ligand excluded by PLIP EOH.71: 3 residues within 4Å: Chain B: Q.345, F.346, N.358 Ligand excluded by PLIP EOH.72: 5 residues within 4Å: Chain B: Y.231, V.406, C.468, N.535, W.600 Ligand excluded by PLIP EOH.75: 1 residues within 4Å: Ligands: EOH.67 Ligand excluded by PLIP EOH.76: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EOH.77: 1 residues within 4Å: Chain B: G.305 Ligand excluded by PLIP EOH.80: 8 residues within 4Å: Chain A: G.627 Chain C: N.334, V.335, M.399, Y.596, Y.597, Y.599 Ligands: EOH.82 Ligand excluded by PLIP EOH.81: 1 residues within 4Å: Chain C: K.372 Ligand excluded by PLIP EOH.82: 7 residues within 4Å: Chain A: G.627, Q.628, Q.629 Chain C: N.334, Y.597, Y.599 Ligands: EOH.80 Ligand excluded by PLIP EOH.83: 1 residues within 4Å: Chain C: D.378 Ligand excluded by PLIP EOH.84: 1 residues within 4Å: Chain C: D.131 Ligand excluded by PLIP EOH.85: 3 residues within 4Å: Chain C: M.360, K.361, N.364 Ligand excluded by PLIP EOH.86: 7 residues within 4Å: Chain C: H.621, H.623, H.672, E.673, F.675, D.676, K.705 Ligand excluded by PLIP EOH.87: 6 residues within 4Å: Chain C: K.113, I.241, I.471, M.525, W.529, D.532 Ligand excluded by PLIP EOH.88: 4 residues within 4Å: Chain A: Q.324, F.342, F.344 Chain C: S.343 Ligand excluded by PLIP EOH.89: 4 residues within 4Å: Chain C: N.41, N.68, K.70, R.77 Ligand excluded by PLIP EOH.90: 2 residues within 4Å: Chain C: A.353, A.354 Ligand excluded by PLIP EOH.91: 6 residues within 4Å: Chain C: Q.382, V.383, L.384, M.385, F.543 Ligands: EOH.100 Ligand excluded by PLIP EOH.92: 3 residues within 4Å: Chain C: N.90, V.451, S.452 Ligand excluded by PLIP EOH.93: 3 residues within 4Å: Chain C: W.607, N.631, A.633 Ligand excluded by PLIP EOH.94: 5 residues within 4Å: Chain B: A.570 Chain C: Y.377, T.415, S.547 Ligands: EOH.107 Ligand excluded by PLIP EOH.95: 5 residues within 4Å: Chain C: D.40, N.41, F.42, H.56, R.77 Ligand excluded by PLIP EOH.96: 3 residues within 4Å: Chain C: A.526, D.532 Ligands: EOH.116 Ligand excluded by PLIP EOH.97: 1 residues within 4Å: Chain C: S.154 Ligand excluded by PLIP EOH.98: 4 residues within 4Å: Chain C: S.189, L.192, N.225, D.236 Ligand excluded by PLIP EOH.99: 2 residues within 4Å: Chain C: D.347 Ligands: EOH.22 Ligand excluded by PLIP EOH.100: 3 residues within 4Å: Chain C: E.388, S.544 Ligands: EOH.91 Ligand excluded by PLIP EOH.101: 3 residues within 4Å: Chain C: Y.492, Y.497, T.504 Ligand excluded by PLIP EOH.102: 5 residues within 4Å: Chain C: F.366, R.367, Q.368, P.380, L.396 Ligand excluded by PLIP EOH.103: 7 residues within 4Å: Chain C: S.622, L.624, R.634, R.670, H.672, F.675, F.699 Ligand excluded by PLIP EOH.104: 4 residues within 4Å: Chain B: S.409, S.547 Chain C: P.569, A.570 Ligand excluded by PLIP EOH.105: 4 residues within 4Å: Chain C: Q.657, N.658, N.659, D.660 Ligand excluded by PLIP EOH.106: 2 residues within 4Å: Chain C: I.49, G.50 Ligand excluded by PLIP EOH.107: 6 residues within 4Å: Chain B: P.569, A.570 Chain C: S.409, N.410, T.415 Ligands: EOH.94 Ligand excluded by PLIP EOH.108: 3 residues within 4Å: Chain A: Q.345 Chain C: Q.324, G.661 Ligand excluded by PLIP EOH.109: 3 residues within 4Å: Chain C: Y.54, P.62, T.63 Ligand excluded by PLIP EOH.110: 3 residues within 4Å: Chain C: K.550, K.589, P.591 Ligand excluded by PLIP EOH.111: 6 residues within 4Å: Chain C: V.31, N.45, P.46, Q.81, A.457, S.458 Ligand excluded by PLIP EOH.112: 3 residues within 4Å: Chain C: G.129, R.130, D.131 Ligand excluded by PLIP EOH.113: 5 residues within 4Å: Chain C: I.178, P.179, E.180, Y.182, P.185 Ligand excluded by PLIP EOH.114: 3 residues within 4Å: Chain C: N.371, D.376, D.378 Ligand excluded by PLIP EOH.115: 3 residues within 4Å: Chain C: D.301, A.303, T.304 Ligand excluded by PLIP EOH.116: 4 residues within 4Å: Chain C: E.118, A.526, C.527 Ligands: EOH.96 Ligand excluded by PLIP EOH.117: 3 residues within 4Å: Chain C: Q.153, L.183, H.184 Ligand excluded by PLIP EOH.118: 2 residues within 4Å: Chain C: A.144, S.145 Ligand excluded by PLIP EOH.119: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EOH.120: 1 residues within 4Å: Chain B: Q.553 Ligand excluded by PLIP EOH.121: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EOH.122: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EOH.125: 3 residues within 4Å: Chain D: G.195, K.197 Ligands: GOL.150 Ligand excluded by PLIP EOH.126: 4 residues within 4Å: Chain D: G.74, E.669, N.671 Ligands: EOH.127 Ligand excluded by PLIP EOH.127: 5 residues within 4Å: Chain D: E.613, E.669, R.670, H.672 Ligands: EOH.126 Ligand excluded by PLIP EOH.128: 2 residues within 4Å: Chain D: Q.368, P.380 Ligand excluded by PLIP EOH.129: 3 residues within 4Å: Chain D: H.623, D.676, F.677 Ligand excluded by PLIP EOH.130: 3 residues within 4Å: Chain D: S.695 Ligands: EOH.137, EOH.138 Ligand excluded by PLIP EOH.131: 4 residues within 4Å: Chain C: H.621, E.673 Chain D: S.579, V.580 Ligand excluded by PLIP EOH.132: 4 residues within 4Å: Chain D: R.349, G.351, F.441, A.443 Ligand excluded by PLIP EOH.133: 5 residues within 4Å: Chain D: G.50, G.51, L.52, E.274, Q.657 Ligand excluded by PLIP EOH.134: 3 residues within 4Å: Chain D: V.383, L.384, F.543 Ligand excluded by PLIP EOH.135: 2 residues within 4Å: Chain D: D.448, D.453 Ligand excluded by PLIP EOH.136: 4 residues within 4Å: Chain D: E.48, I.49, D.453, T.456 Ligand excluded by PLIP EOH.137: 3 residues within 4Å: Chain D: P.697 Ligands: EOH.130, EOH.138 Ligand excluded by PLIP EOH.138: 6 residues within 4Å: Chain D: F.677, E.679, S.695, P.697 Ligands: EOH.130, EOH.137 Ligand excluded by PLIP EOH.139: 8 residues within 4Å: Chain B: G.627 Chain D: N.334, V.335, M.399, Y.596, Y.597, S.598, Y.599 Ligand excluded by PLIP EOH.140: 9 residues within 4Å: Chain D: K.113, I.241, V.266, G.267, S.268, I.471, E.472, T.522, M.525 Ligand excluded by PLIP EOH.141: 5 residues within 4Å: Chain D: N.125, Y.128, K.372, E.420, Q.478 Ligand excluded by PLIP EOH.142: 3 residues within 4Å: Chain D: Y.363, G.434, E.438 Ligand excluded by PLIP EOH.143: 3 residues within 4Å: Chain D: G.351, S.352, A.353 Ligand excluded by PLIP EOH.144: 3 residues within 4Å: Chain D: V.171, N.177 Ligands: EOH.152 Ligand excluded by PLIP EOH.145: 8 residues within 4Å: Chain D: S.196, G.220, F.221, A.222, Q.530, V.643, E.644, W.646 Ligand excluded by PLIP EOH.146: 1 residues within 4Å: Chain D: G.375 Ligand excluded by PLIP EOH.147: 3 residues within 4Å: Chain C: E.617 Chain D: Q.577, S.578 Ligand excluded by PLIP EOH.148: 3 residues within 4Å: Chain D: Q.345, F.346, N.358 Ligand excluded by PLIP EOH.149: 5 residues within 4Å: Chain D: Y.231, V.406, C.468, N.535, W.600 Ligand excluded by PLIP EOH.152: 1 residues within 4Å: Ligands: EOH.144 Ligand excluded by PLIP EOH.153: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EOH.154: 1 residues within 4Å: Chain D: G.305 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.73: 5 residues within 4Å: Chain B: Q.194, G.195, E.644 Ligands: EOH.48, GOL.74 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.195 GOL.74: 5 residues within 4Å: Chain B: Q.194, S.640, E.644 Chain D: E.690 Ligands: GOL.73 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Q.194, B:G.195, B:S.640, B:E.644, D:E.690 GOL.150: 5 residues within 4Å: Chain D: Q.194, G.195, E.644 Ligands: EOH.125, GOL.151 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.195 GOL.151: 5 residues within 4Å: Chain B: E.690 Chain D: Q.194, S.640, E.644 Ligands: GOL.150 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:E.690, D:Q.194, D:G.195, D:S.640

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Medrano, F.J. et al., Structure of the Epsilon-Lysine Oxidase from Marinomonas Mediterranea. To be Published

Release Date

2013-10-23

Peptides

L-LYSINE 6-OXIDASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

L-LYSINE 6-OXIDASE