SMTL ID : 6hqv.1

Pentafunctional AROM Complex from Chaetomium thermophilum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 30 residues within 4Å: Chain A: D.56, N.58, L.59, P.88, G.89, E.90, K.93, G.121, G.122, V.123, D.126, T.146, T.147, L.149, D.153, S.154, K.159, K.168, N.169, F.186, T.189, L.190, P.191, E.194, N.197, E.201, K.257, H.294 Ligands: ZN.2, GLU.3 21 PLIP interactions: 20 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:L.149 Hydrogen bonds: A:D.56, A:N.58, A:G.89, A:E.90, A:K.93, A:G.121, A:G.122, A:V.123, A:D.126, A:T.146, A:T.147, A:K.168, A:K.168, A:N.169, A:T.189, A:T.189, A:E.194, A:N.197, A:K.257, E.3 NAD.11: 30 residues within 4Å: Chain B: D.56, N.58, L.59, P.88, G.89, E.90, K.93, G.121, G.122, V.123, D.126, T.146, T.147, L.149, D.153, S.154, K.159, K.168, N.169, F.186, T.189, L.190, P.191, E.194, N.197, E.201, K.257, H.294 Ligands: ZN.12, GLU.13 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.149 Hydrogen bonds: B:D.56, B:N.58, B:G.89, B:E.90, B:K.93, B:G.121, B:G.122, B:V.123, B:D.126, B:T.146, B:K.168, B:K.168, B:N.169, B:N.197, B:K.257

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: D.153, E.201, H.278, H.294 Ligands: NAD.1, GLU.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.201, A:H.278, A:H.294, GLU.3 ZN.12: 6 residues within 4Å: Chain B: D.153, E.201, H.278, H.294 Ligands: NAD.11, GLU.13 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:E.201, B:H.278, B:H.294, GLU.13

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.3: 14 residues within 4Å: Chain A: D.153, K.159, N.169, E.201, K.204, K.257, R.271, L.274, N.275, H.278, H.294 Ligands: NAD.1, ZN.2, PO4.4 13 PLIP interactions: 10 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:K.159 Hydrogen bonds: A:D.153, A:N.169, A:K.204, E.3, E.3, E.3 Salt bridges: A:K.159, A:K.257, A:R.271, A:H.278, A:H.282, A:H.294 GLU.13: 13 residues within 4Å: Chain B: D.153, K.159, E.201, K.204, K.257, R.271, L.274, N.275, H.278, H.294 Ligands: NAD.11, ZN.12, PO4.14 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:K.159 Hydrogen bonds: B:D.153, B:R.271 Salt bridges: B:K.159, B:K.257, B:R.271, B:H.278, B:H.282, B:H.294

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

PO4.4: 7 residues within 4Å: Chain A: K.159, N.169, N.275, H.282, K.363 Chain B: R.137 Ligands: GLU.3 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.169, A:N.275, A:N.275 Salt bridges: A:K.159, A:H.282, A:K.363, B:R.137 PO4.8: 8 residues within 4Å: Chain A: M.876, R.877, G.878, A.879, G.880, K.881, S.882, T.883 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.878, A:G.880, A:K.881, A:S.882, A:T.883 PO4.10: 5 residues within 4Å: Chain A: D.726, E.754, R.757, H.802, R.803 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.726, A:E.754 Salt bridges: A:R.757, A:H.802, A:R.803, A:K.829 PO4.14: 7 residues within 4Å: Chain A: R.137 Chain B: K.159, N.169, N.275, H.282, K.363 Ligands: GLU.13 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.169, B:N.275 Salt bridges: B:K.159, B:H.282, B:K.363, A:R.137 PO4.19: 5 residues within 4Å: Chain B: D.726, E.754, R.757, H.802, R.803 4 PLIP interactions: 4 interactions with chain B Salt bridges: B:R.757, B:H.802, B:R.803, B:K.829

2 x 3DS: (4S,5R)-4,5-dihydroxy-3-oxocyclohex-1-ene-1-carboxylic acid(Covalent)

3DS.5: 14 residues within 4Å: Chain A: S.1062, E.1086, R.1088, T.1118, R.1120, H.1179, K.1207, L.1240, M.1242, R.1250, P.1258, A.1268, A.1269, Q.1272 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:K.1207, A:P.1258, A:A.1268 Hydrogen bonds: A:S.1062, A:R.1088, A:R.1120, A:K.1207, A:Q.1272 Salt bridges: A:K.1207, A:R.1250 3DS.15: 13 residues within 4Å: Chain B: S.1062, E.1086, R.1088, T.1118, R.1120, H.1179, K.1207, M.1242, R.1250, P.1258, A.1268, A.1269, Q.1272 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:K.1207, B:P.1258, B:A.1268 Hydrogen bonds: B:S.1062, B:R.1088, B:R.1120, B:K.1207, B:Q.1272 Salt bridges: B:K.1207, B:R.1250

6 x SKM: (3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID(Non-covalent)

SKM.6: 12 residues within 4Å: Chain A: L.1295, S.1303, S.1305, S.1347, V.1348, T.1349, K.1353, N.1374, D.1394, Y.1524, Q.1552, Q.1556 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.1305, A:K.1353, A:K.1353, A:N.1374, A:N.1374, A:Y.1524, A:Y.1524, A:Q.1552, A:Q.1556 SKM.7: 6 residues within 4Å: Chain A: D.900, R.925, G.948, G.949, G.950, R.1005 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.900, A:E.928, A:G.949 Salt bridges: A:R.925, A:R.1005 SKM.9: 6 residues within 4Å: Chain A: S.423, R.427, T.497, S.576, Q.577, Y.607 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.423, A:S.576, A:Q.577 Salt bridges: A:R.427 SKM.16: 12 residues within 4Å: Chain B: S.1303, S.1305, S.1347, V.1348, T.1349, K.1353, N.1374, D.1394, Y.1524, L.1549, Q.1552, Q.1556 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.1305, B:S.1305, B:T.1349, B:K.1353, B:K.1353, B:N.1374, B:N.1374, B:Y.1524, B:Q.1552, B:Q.1556 SKM.17: 9 residues within 4Å: Chain B: D.900, I.911, F.924, R.925, E.928, G.948, G.949, G.950, R.1005 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.900, B:E.928, B:G.949 Salt bridges: B:R.925, B:R.1005 SKM.18: 6 residues within 4Å: Chain B: S.423, R.427, T.497, S.576, Q.577, Y.607 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.607 Hydrogen bonds: B:S.576, B:S.576 Salt bridges: B:R.427

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arora Veraszto, H. et al., Architecture and functional dynamics of the pentafunctional AROM complex. Nat.Chem.Biol. (2020)

Release Date

2020-05-06

Peptides

Pentafunctional AROM polypeptide: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pentafunctional AROM polypeptide