SMTL ID : 7cjo.1

Crystal structure of metal-bound state of glucose isomerase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 12 residues within 4Å: Chain A: W.16, H.54, T.90, T.91, F.94, V.135, W.137, E.181, N.215, D.245, D.287 Ligands: MG.12 Ligand excluded by PLIP EDO.2: 12 residues within 4Å: Chain A: P.97, V.98, F.99, K.100, D.101, D.108, V.111 Chain B: R.334, A.365, A.366, R.368, M.370 Ligand excluded by PLIP EDO.3: 9 residues within 4Å: Chain A: L.93, G.103, F.104, A.115, A.136, W.137, G.138, E.141, F.162 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: D.124, V.127, E.128, Y.174 Ligand excluded by PLIP EDO.5: 11 residues within 4Å: Chain A: G.146, G.147, A.148, K.149, D.150, V.151 Chain B: W.270, F.320, R.321, L.330, L.335 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: D.9, R.10, F.11, E.276, R.284, Y.310, L.311, K.314 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: D.353, S.355, A.356 Chain B: R.109, D.110, R.113 Ligand excluded by PLIP EDO.8: 9 residues within 4Å: Chain A: V.151, L.155, L.192, L.193, P.194, H.198 Chain B: H.230, G.231, Q.234 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: Q.21, R.23, A.29, T.30, R.31, R.32 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: R.68, E.69, V.72, L.125, E.128 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: D.156, K.159, R.205 Chain B: W.237, A.238 Ligand excluded by PLIP EDO.14: 13 residues within 4Å: Chain A: R.334, A.365, A.366, R.368, M.370 Chain B: P.97, V.98, F.99, K.100, D.101, A.106, D.108, V.111 Ligand excluded by PLIP EDO.15: 11 residues within 4Å: Chain A: W.270, D.273, R.321, L.330, L.335 Chain B: G.146, G.147, A.148, K.149, D.150, V.151 Ligand excluded by PLIP EDO.16: 11 residues within 4Å: Chain B: W.16, H.54, T.90, F.94, V.135, W.137, E.181, N.215, D.245, D.287 Ligands: MG.24 Ligand excluded by PLIP EDO.17: 8 residues within 4Å: Chain B: D.9, R.10, F.11, E.276, R.284, Y.310, L.311, K.314 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain B: G.19, W.20, Q.21, G.22, R.23 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain B: W.16, H.54, D.56, D.57, N.92, F.94, T.95 Ligand excluded by PLIP EDO.20: 9 residues within 4Å: Chain B: L.93, G.103, F.104, A.115, A.136, W.137, G.138, E.141, F.162 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: W.237, A.238 Chain B: D.156, K.159, R.205 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain B: R.42, E.45, L.46, W.300 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: R.76, L.79, D.80, E.128, L.129 Ligand excluded by PLIP EDO.26: 12 residues within 4Å: Chain C: W.16, H.54, T.90, T.91, F.94, V.135, W.137, E.181, N.215, D.245, D.287 Ligands: MG.37 Ligand excluded by PLIP EDO.27: 12 residues within 4Å: Chain C: P.97, V.98, F.99, K.100, D.101, D.108, V.111 Chain D: R.334, A.365, A.366, R.368, M.370 Ligand excluded by PLIP EDO.28: 9 residues within 4Å: Chain C: L.93, G.103, F.104, A.115, A.136, W.137, G.138, E.141, F.162 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain C: D.124, V.127, E.128, Y.174 Ligand excluded by PLIP EDO.30: 11 residues within 4Å: Chain C: G.146, G.147, A.148, K.149, D.150, V.151 Chain D: W.270, F.320, R.321, L.330, L.335 Ligand excluded by PLIP EDO.31: 8 residues within 4Å: Chain C: D.9, R.10, F.11, E.276, R.284, Y.310, L.311, K.314 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain C: D.353, S.355, A.356 Chain D: R.109, D.110, R.113 Ligand excluded by PLIP EDO.33: 9 residues within 4Å: Chain C: V.151, L.155, L.192, L.193, P.194, H.198 Chain D: H.230, G.231, Q.234 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain C: Q.21, R.23, A.29, T.30, R.31, R.32 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain C: R.68, E.69, V.72, L.125, E.128 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain C: D.156, K.159, R.205 Chain D: W.237, A.238 Ligand excluded by PLIP EDO.39: 13 residues within 4Å: Chain C: R.334, A.365, A.366, R.368, M.370 Chain D: P.97, V.98, F.99, K.100, D.101, A.106, D.108, V.111 Ligand excluded by PLIP EDO.40: 11 residues within 4Å: Chain C: W.270, D.273, R.321, L.330, L.335 Chain D: G.146, G.147, A.148, K.149, D.150, V.151 Ligand excluded by PLIP EDO.41: 11 residues within 4Å: Chain D: W.16, H.54, T.90, F.94, V.135, W.137, E.181, N.215, D.245, D.287 Ligands: MG.49 Ligand excluded by PLIP EDO.42: 8 residues within 4Å: Chain D: D.9, R.10, F.11, E.276, R.284, Y.310, L.311, K.314 Ligand excluded by PLIP EDO.43: 5 residues within 4Å: Chain D: G.19, W.20, Q.21, G.22, R.23 Ligand excluded by PLIP EDO.44: 7 residues within 4Å: Chain D: W.16, H.54, D.56, D.57, N.92, F.94, T.95 Ligand excluded by PLIP EDO.45: 9 residues within 4Å: Chain D: L.93, G.103, F.104, A.115, A.136, W.137, G.138, E.141, F.162 Ligand excluded by PLIP EDO.46: 5 residues within 4Å: Chain C: W.237, A.238 Chain D: D.156, K.159, R.205 Ligand excluded by PLIP EDO.47: 4 residues within 4Å: Chain D: R.42, E.45, L.46, W.300 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain D: R.76, L.79, D.80, E.128, L.129 Ligand excluded by PLIP

8 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 6 residues within 4Å: Chain A: E.181, E.217, H.220, D.245, D.287 Ligands: EDO.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.181, A:E.217, A:D.245, A:D.287, H2O.7 MG.13: 6 residues within 4Å: Chain A: K.183, E.217, H.220, N.247, D.255, D.257 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.217, A:H.220, A:D.255, A:D.257, H2O.9 MG.24: 6 residues within 4Å: Chain B: E.181, E.217, H.220, D.245, D.287 Ligands: EDO.16 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.181, B:E.217, B:D.245, B:D.287 MG.25: 6 residues within 4Å: Chain B: K.183, E.217, H.220, N.247, D.255, D.257 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.217, B:H.220, B:D.255, B:D.257, H2O.24 MG.37: 6 residues within 4Å: Chain C: E.181, E.217, H.220, D.245, D.287 Ligands: EDO.26 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.181, C:E.217, C:D.245, C:D.287, H2O.37 MG.38: 6 residues within 4Å: Chain C: K.183, E.217, H.220, N.247, D.255, D.257 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.217, C:H.220, C:D.255, C:D.257, H2O.40 MG.49: 6 residues within 4Å: Chain D: E.181, E.217, H.220, D.245, D.287 Ligands: EDO.41 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.181, D:E.217, D:D.245, D:D.287 MG.50: 6 residues within 4Å: Chain D: K.183, E.217, H.220, N.247, D.255, D.257 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.217, D:H.220, D:D.255, D:D.257, H2O.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nam, K.H., Crystal structure of the metal-free state of glucose isomerase reveals its minimal open configuration for metal binding. Biochem.Biophys.Res.Commun. (2021)

Release Date

2021-07-14

Peptides

Xylose isomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Xylose isomerase

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