SMTL ID : 2a5h.1

2.1 Angstrom X-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale SB4, with Michaelis analog (L-alpha-lysine external aldimine form of pyridoxal-5'-phosphate).

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.268, V.271 Chain B: C.375, C.377, C.380 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Metal complexes: A:C.268, B:C.375, B:C.377, B:C.380 ZN.7: 5 residues within 4Å: Chain A: C.375, C.377, C.380 Chain B: C.268, V.271 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Metal complexes: B:C.268, A:C.375, A:C.377, A:C.380 ZN.14: 5 residues within 4Å: Chain C: C.268, V.271 Chain D: C.375, C.377, C.380 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Metal complexes: C:C.268, D:C.375, D:C.377, D:C.380 ZN.20: 5 residues within 4Å: Chain C: C.375, C.377, C.380 Chain D: C.268, V.271 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Metal complexes: C:C.375, C:C.377, C:C.380, D:C.268

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: H.111, R.112, Y.113 Chain D: R.409 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.111 SO4.8: 7 residues within 4Å: Chain B: H.111, R.112, Y.113, P.114, Q.162 Chain C: E.408, R.409 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.111 SO4.13: 5 residues within 4Å: Chain B: E.408, R.409 Chain C: H.111, R.112, Y.113 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.112 Salt bridges: C:H.111 SO4.19: 6 residues within 4Å: Chain A: E.408, R.409 Chain D: H.111, R.112, Y.113, P.114 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.162 Salt bridges: D:H.111

4 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.3: 19 residues within 4Å: Chain A: H.131, C.132, T.133, R.134, S.169, G.170, G.171, G.200, T.229, H.230, Q.258, V.260, Y.290, Q.291, C.292, D.293, L.298 Ligands: LYS.4, SF4.6 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.131, A:T.133, A:T.133, A:Q.258, A:Q.258, A:D.293 Water bridges: A:S.201, A:T.229 Salt bridges: A:H.230 SAM.9: 19 residues within 4Å: Chain B: H.131, C.132, T.133, R.134, S.169, G.170, G.171, G.200, R.202, H.230, Q.258, V.260, Y.290, Q.291, C.292, D.293, L.298 Ligands: LYS.10, SF4.12 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:H.131, B:T.133, B:T.133, B:Q.258, B:Q.258, B:D.293 Water bridges: B:S.201, B:T.229 Salt bridges: B:H.230 SAM.15: 19 residues within 4Å: Chain C: H.131, C.132, T.133, R.134, S.169, G.170, G.171, G.200, R.202, H.230, Q.258, V.260, Y.290, Q.291, C.292, D.293, L.298 Ligands: LYS.16, SF4.18 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:H.131, C:T.133, C:G.171, C:Q.258, C:Q.258, C:D.293 Water bridges: C:S.201, C:T.229 Salt bridges: C:H.230 SAM.21: 20 residues within 4Å: Chain D: H.131, C.132, T.133, R.134, S.169, G.170, G.171, G.200, R.202, T.229, H.230, Q.258, V.260, Y.290, Q.291, C.292, D.293, L.298 Ligands: LYS.22, SF4.24 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:H.131, D:T.133, D:Q.258, D:Q.258, D:D.293 Water bridges: D:S.201, D:T.229 Salt bridges: D:H.230

4 x LYS: LYSINE(Non-covalent)

LYS.4: 12 residues within 4Å: Chain A: L.98, L.118, T.133, R.134, L.167, S.169, Q.258, Y.290, D.293, D.330 Ligands: SAM.3, PLP.5 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:Y.290 Hydrogen bonds: A:S.169, A:D.293, A:D.330 Water bridges: A:R.198, A:Q.258 Salt bridges: A:R.134 LYS.10: 11 residues within 4Å: Chain B: L.98, L.118, R.134, L.167, S.169, Q.258, Y.290, D.293, D.330 Ligands: SAM.9, PLP.11 7 PLIP interactions: 7 interactions with chain B, Hydrophobic interactions: B:Y.290 Hydrogen bonds: B:S.169, B:D.293, B:D.330 Water bridges: B:Q.258, B:K.337 Salt bridges: B:R.134 LYS.16: 12 residues within 4Å: Chain C: L.98, L.118, T.133, R.134, L.167, S.169, Q.258, Y.290, D.293, D.330 Ligands: SAM.15, PLP.17 7 PLIP interactions: 7 interactions with chain C, Hydrophobic interactions: C:Y.290 Hydrogen bonds: C:S.169, C:D.330 Water bridges: C:R.198, C:Q.258, C:K.337 Salt bridges: C:R.134 LYS.22: 11 residues within 4Å: Chain D: L.98, L.118, R.134, L.167, S.169, Q.258, Y.290, D.293, D.330 Ligands: SAM.21, PLP.23 6 PLIP interactions: 6 interactions with chain D, Hydrophobic interactions: D:Y.290 Hydrogen bonds: D:S.169, D:D.293 Water bridges: D:Q.258, D:Y.290 Salt bridges: D:R.134

4 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.5: 12 residues within 4Å: Chain A: T.110, Y.113, R.116, L.118, L.167, R.198, Y.287, Y.288, K.337 Chain B: S.320, G.321 Ligands: LYS.4 13 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:T.110, A:Y.113, A:L.118, A:L.167, K.4 Hydrogen bonds: A:R.112, B:G.321 Water bridges: A:R.116, A:R.134, A:R.198 Salt bridges: A:R.116, A:R.198, A:K.337 PLP.11: 13 residues within 4Å: Chain A: S.320, G.321 Chain B: T.110, R.112, Y.113, R.116, L.118, L.167, R.198, Y.287, Y.288, K.337 Ligands: LYS.10 15 PLIP interactions: 13 interactions with chain B, 1 Ligand-Ligand interactions, 1 interactions with chain A Hydrophobic interactions: B:T.110, B:L.118, B:L.167, K.10 Hydrogen bonds: B:R.112, A:G.321 Water bridges: B:R.116, B:R.116, B:R.134, B:R.198, B:R.198, B:K.337 Salt bridges: B:R.116, B:R.198, B:K.337 PLP.17: 12 residues within 4Å: Chain C: T.110, Y.113, R.116, L.118, L.167, R.198, Y.287, Y.288, K.337 Chain D: S.320, G.321 Ligands: LYS.16 16 PLIP interactions: 14 interactions with chain C, 1 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: C:T.110, C:L.118, C:L.167, K.16 Hydrogen bonds: C:R.112, C:Y.287, C:Y.288, D:G.321 Water bridges: C:R.116, C:R.116, C:R.134, C:R.198, C:K.337 Salt bridges: C:R.116, C:R.198, C:K.337 PLP.23: 13 residues within 4Å: Chain C: S.320, G.321 Chain D: T.110, R.112, Y.113, R.116, L.118, L.167, R.198, Y.287, Y.288, K.337 Ligands: LYS.22 15 PLIP interactions: 13 interactions with chain D, 1 Ligand-Ligand interactions, 1 interactions with chain C Hydrophobic interactions: D:T.110, D:L.118, D:L.167, K.22 Hydrogen bonds: D:R.112, D:Y.287, D:Y.288, C:G.321 Water bridges: D:R.112, D:R.112, D:R.198, D:K.337 Salt bridges: D:R.116, D:R.198, D:K.337

4 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.6: 8 residues within 4Å: Chain A: C.125, C.129, C.132, G.170, G.171, R.202, H.230 Ligands: SAM.3 4 PLIP interactions: 4 interactions with chain A, Salt bridges: A:D.172 Metal complexes: A:C.125, A:C.129, A:C.132 SF4.12: 8 residues within 4Å: Chain B: C.125, C.129, C.132, G.170, G.171, R.202, H.230 Ligands: SAM.9 4 PLIP interactions: 4 interactions with chain B, Salt bridges: B:D.172 Metal complexes: B:C.125, B:C.129, B:C.132 SF4.18: 8 residues within 4Å: Chain C: C.125, C.129, C.132, G.170, G.171, R.202, H.230 Ligands: SAM.15 4 PLIP interactions: 4 interactions with chain C, Salt bridges: C:D.172 Metal complexes: C:C.125, C:C.129, C:C.132 SF4.24: 9 residues within 4Å: Chain D: C.125, Y.128, C.129, C.132, G.170, G.171, R.202, H.230 Ligands: SAM.21 4 PLIP interactions: 4 interactions with chain D, Salt bridges: D:D.172 Metal complexes: D:C.125, D:C.129, D:C.132

Links

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Citation

Lepore, B.W. et al., The X-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale. Proc.Natl.Acad.Sci.Usa (2005)

Release Date

2005-10-04

Peptides

L-lysine 2,3-aminomutase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

L-lysine 2,3-aminomutase